NCBI HomeEntrez Gene

Entrez Gene: Integrated Access to Genes of Genomes in the Reference Sequence Collection

Introduction

With the increasing sequencing and annotation of key genomes, having a gene-based view of the resultant information is useful. Entrez Gene has therefore been implemented to supply key connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to any gene with defining sequence, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are tracked, and information is added when available. Entrez Gene can be considered as the successor to LocusLink, with the major differences being in greater scope (more of the genomes represented by NCBI Reference Sequences or RefSeqs) and in being integrated for indexing and query in NCBI's Entrez system.

To help you use Entrez Gene effectively, this document is divided into the following sections:

1. Maintaining the Data
2. Interpreting the Display
3. Query Tips with Examples
4. Tips for the Programmer

Previous users of LocusLink may find the subsections Tips for Previous LocusLink Users helpful.

Maintaining the Data

New Records

Records are added to Gene if any of the following conditions is met:

• A RefSeq is created for a completely sequenced genome and that record contains annotated genes. In the case of RNA viruses with polyprotein precursors, annotated proteins are treated as equivalent to a 'gene'.
• A recognized genome-specific database provides information about genes (preferably with defining sequence) or mapped phenotypes.
• The NCBI Genome Annotation Pipeline reports model genes.

Gene records are not created for genomes incompletely represented by whole genome shotgun (WGS) assemblies, which are provided in terms of RefSeqs by the accessions of the pattern NZ_ABCD12345678.

The minimum set of data necessary for a gene record, therefore, is a unique identifier or GeneID assigned by NCBI, a preferred symbol, and any sequence information, map information, or official nomenclature from an authority list.

Updated Records

Existing records are updated when new information is received. For some genomes, this may occur when a genome is reannotated and corresponding RefSeqs are updated. For other genomes, this may occur when any information attached to a gene record is altered. At present, updates are processed twice weekly, with refreshed data appearing Tuesdays and Thursdays.

GeneRIFs, although displayed as part of a Gene record, are processed independently of the Gene record itself. The majority of records is supplied by the NLM Index Section, and are integrated weekly. Those are available with the first update to Gene within a week.

The modification date, therefore, will be the later of any update to Gene or the GeneRIF supplement.

All previous records will be searchable in Gene by the GeneID only. If it is known that the suppressed record has been replaced with another, the URL to the current record is provided. This is of particular benefit to those interested in retrieving information about NCBI Gene predictions that have not been retained.

Tips for Previous Users of LocusLink

Display of all discontinued records, replaced or not, is an added function compared to LocusLink. In LocusLink, only replaced records, and a subset of discontinued records, could be retrieved.

Interpreting the Display

This section is divided according to the Display options provided by Entrez:

• Default (same as Graphic)
• Summary
• Brief
• ASN.1
• XML
• Graphic (same as Default)
• Gene Table
• UI List
• LinkOut
• Book Links
• Geo Links
• Nucleotide Links
• OMIM Links
• Protein Links
• PubMed Links
• SNP Links
• Taxonomy Links
• UniGene Links
• UniSTS Links

Summary Display

When you process a query, the result is displayed in the Summary format. You can see this by noting the word Summary in the Display box.

The summary display (Figure 1) provides a check box for selecting records to display, the preferred symbol, the complete full name if available, the binomial for the species (in square brackets), genomic location, and the GeneID. If the gene is on a named plasmid, then the plasmid name will be given as the location. The Links, provided at the right, support ready display of related records in Entrez, as documented in Table 1. To navigate to more information about specific records, check the records to display (the default being all) and select the display option in the gray query bar.

Figure 1. Sample Summary Display.

A summary display (Note display option set to Summary.) for the query homeo box homolog. When available, Gene uses the title for a gene supplied by the appropriate nomenclature committee. In this example, note that some nomenclature committees include, as part of their official name, information about the species that was used to define the name of the homolog. That part of the title is usually given in parentheses, and should not be confused with the binomial for the source genome, which is italicized and in square brackets.

Tips for Previous Users of LocusLink
The summary display format corresponds most closely to what was termed the Brief Display option in LocusLink, with the LocusID, symbol, species, full description, location, and array of colored boxes indicating available links. In Gene, there is no link from the location information to Map Viewer; that is provided in the Links menu instead. The array of colored boxes is also replaced by the Links menu.

The Summary Display option of LocusLink, which reported all alternate symbols and sequence accessions associated with a gene record, is not currently provided from Gene.

Brief Display

The functions allowed from the brief display are similar to those described from the summary display described in the previous section. This purpose of the Brief option is to support a more compact result set, while providing enough information (the preferred symbol, 20 characters of the full name, and the GeneID) to allow you to select records to display in full. The Links provided at the right of the display support ready display of related records in Entrez, including: Nucleotide sequences, Protein sequences, Books, GEO, HomoloGene, OMIM, SNP, UniGene, UniSTS, and Taxonomy. To see more information, check the records to display (the default being all), and select the display option in the grey query bar.

Tips for Previous Users of LocusLink

There is no exact precedent in LocusLink. The links in the Links menu at the right correspond to the color-coded links in LocusLink (Table 1), but there are many more in Entrez Gene than LocusLink supplied.

Default (Graphic) Display

• Title and Links
• Transcripts and Products
• Genomic Context
• Description
• Bibliography
• General Gene Information
• NCBI Reference Sequences (RefSeqs)
• Related Sequences
• Additional Links

Title and Links

The NCBI GeneID and the Locus tag for the record are in the next line. Locus tag corresponds to the systematic feature qualifier used by the international sequence collaboration (DDBJ/EMBL/GenBank), and can be assigned by sequence submitters as a unique, systematic gene descriptor. When such a value is not available from submitted sequence, the identifier from a collaborating model organism database is used. Locus tag is often used to anchor a link to a database other than Entrez Gene.

The second line also includes the last date a record was changed in the format day-month-year. Change is defined as any modification to the content of the record, including ancillary changes such as the URL for a displayed link.

Transcripts and Products

This section is provided when a gene has been annotated on a genomic RefSeq, in other words when the intron/exon/coding region information is available in genomic coordinates. Each position of a gene product, when represented by a RefSeq RNA (accession NM_000000 or XM_000000 for mRNA, NR_000000 or XR_000000 for non-protein coding RNAs) and/or protein (NP_000000 or XP_000000), is provided relative to the genomic accession on which it is annotated. Each accession is an anchor to a menu allowing display of the sequence in several formats. Protein accessions also facilitate retrieval of specific BLink, CDD, or COG displays. Using the following figure as an example (interactive view):

Accessing the Genomic Sequence

NC_000010 is the accession of the genomic contig that contains the gene. The region being shown in this accession is indicated by the integers to the left and right of the accession. The rightward pointing arrow indicates that these mRNAs are annotated in the same orientation as the NC accession (Since this is an example of a human chromosome, pter->qter). If mRNA is annotated on the reverse complement of the genomic sequence, then the phrase (shown on reverse complement genome) is printed. RefSeq below provides a link to the RefSeq section where there may be more information about these sequences.

Clicking on the accession NC_000010 brings up a menu that facilitates navigation to:

• FASTA - the genomic sequence of the specified range, in the default orientation [not necessarily that of the annotation], in FASTA format
• GENBANK - the genomic sequence of the specified range, in the default orientation [not necessarily that of the annotation], in GenBank format
• GRAPHIC - the genomic sequence of the specified range, in the default orientation [not necessarily that of the annotation], in graphic format

When you have used any of the above links to display the genomic sequence of the gene displayed on the record (in this case human PAX2), you can use standard Entrez functions to:

• Download the sequence in any format using the desired combination of Display and Send to options.
• Modify the limits of the sequence to be displayed or downloaded using the Get Subsequence option.
• Add or suppress the display of optional features using the Features option.

Display of Products and Accessing their Sequences

If there are accessions listed at the left of the diagram (e.g. NM_003987, NM_003989, etc.), these represent RefSeq RNAs. Each accession anchors a link to retrieving sequence, formatted as described (FASTA, GENBANK, and GRAPHIC) for the genomic RefSeq. If there are accessions listed at the right, these are for encoded proteins. In addition to supporting links to sequence, the protein accessions facilitate connections to protein-specific tools or displays, such as

• BLink (BLAST Link), which displays the results of BLAST searches that have been done for every protein sequence in the Entrez Proteins data domain, and supports multiple tools for comparing proteins
• CDD (Conserved Domain Database), which allows review of domains found in the protein, as well as links to records of other proteins with a related domain

Each protein accession may also have a distinguishing label. In this example, these are the isoform designations, isoforms a, b, c, and d.

The labels of the RNA and protein accessions are color coded to coincide with the diagram of the placement of the exons. Blue indicates RNA, and in protein-coding genes, the untranslated region (UTR) of any exon. Maroon indicates protein, and therefore is used to represent the coding region of an exon. If an intron is flanked by coding sequence, then the line connecting the exons is maroon; otherwise, it is blue.

Genomic Context

The genomic context section reports the location of the gene on the chromosome in non-sequence coordinates and the strain and genotype information of the source sequence. If the gene has been included in a genomic annotation, the section also diagrams neighboring genes and indicates either orientation. If the name of a gene is too long to use for a label, truncation is indicated by an ellipsis (...). The gene being shown on the diagram is in maroon. All other diagrams and labels anchor links to specific gene pages, supporting quick navigation to review neighboring genes by clicking in the area of the symbol/arrow.

If a gene has not been included in the current version of the annotated genome provided in NCBI RefSeqs, the Genomic Context section will not include a diagram, but will report the map location. If the gene is annotated on more than one genomic RefSeq, only one will be used for the graphic display, but the location information will be provided in the ASN.1 of the record.

Description

The next section includes several categories of information for each gene as available. These include:

1. Gene type. Possible values are tRNA, rRNA, snRNA, scRNA, snoRNA, miscRNA, protein-coding, pseudo, other, and unknown.
   These are indexed as properties of a gene via the terms:
   • genetype trna
   • genetype rrna
   • genetype snrna
   • genetype scrna
   • genetype snorna
   • genetype miscrna
   • genetype protein coding
   • genetype pseudo
   • genetype other
   • genetype unknown

   More details about Gene Types are in the related subsection describing what is indexed by Gene as a property.

2. Gene or RNA name. The name assigned to the gene or its primary RNA product.
3. RefSeq status. Any of the set of status descriptions defined by RefSeq.
4. Organism. The binomial, and strain when appropriate, with a link to the NCBI Taxonomy database.
5. Lineage. Binomial and lineage from the Taxonomy database.
6. Summary. Descriptive text about the gene, its cellular localization, its function, and its effect on phenotype.
7. Gene Aliases. Unofficial symbols and descriptions that have been used for this gene and its products. If there is no official symbol, the symbol at the top of the display is repeated in this section.
8. General Protein Information.
   Name: the default protein name.
   Description. Additional descriptive text.

Bibliography

The Bibliography section provides a link to PubMed in the same format as that generated from the PubMed option in the pull-down Links menu at the upper right portion of the page.

If GeneRIFs have been submitted, they are included in this section. The majority of these annotations have been provided via a collaboration between the NLM's MedLine indexing staff and NCBI. The GeneRIF home page provides more information about the project, including how general users can make submissions.

General Gene Information

This section includes several subcategories of information, including:

1. GeneOntology (GO). The GO terms are listed by source of the information, category, term, evidence information, and links to supporting publications. The GO term supports a link to the AmiGO browser.
2. Homology. A partial listing, with links, of orthologs in other species. Other views of homology data are available from TaxPlot and the HomoloGene link in the Links menu.
3. Phenotypes. A description of the effect of the gene on phenotype, especially disease. Links to more information are provided as available, as in the case of human disease and links to OMIM.
4. Markers. An enumeration of the markers that are related to this gene. The relationship is reported based either on direct reports, e-PCR using mRNA templates, or e-PCR-based localization on the genome withing a region beginning 2 kb upstream of the gene and ending 0.5 kb downstream. Links are provided the NCBI UniSTS database.
5. Pathways. A description of pathways that include this gene with links to more information about that pathway.
6. Relationships. At present, used for gene models to describe some of the related sequences used to support the model transcript.

NCBI Reference Sequences (RefSeqs)

This section describes the gene-specific NCBI reference sequences (RefSeqs) that have been established for this gene. In addition to enumerating the accessions and providing links to the appropriate Entrez sequence database, this section may also include descriptions of each transcript variant, accessions of the public sequences used to support any transcript, and a listing of computed domains in an encoded protein. The text provided in this section therefore supports retrieving gene records based on descriptions of conserved domains.

Related Sequences

This section lists nucleotide and protein accessions that are related to the gene, and provides links to the appropriate sequence record in Entrez nucleotide or protein. If the protein sequence record is not part of a set of a nucleotide record and the protein it encodes, the word 'none' is printed in the Nucleotide column. The type of nucleotide record is printed before the nucleotide accession, and the strain is printed after the protein accession, as applicable.

Additional Links

This section provides a printable view of a subset of links to information both within and external to NCBI. Some of these links overlap those included in the Links menu. The intent of this section is to provide a printable report of, for example, MIM numbers, UniGene cluster numbers, and family-specific Web sites.

Tips for Previous Users of LocusLink

Table 2
Where to find the content of a LocusLink report page in Entrez Gene

LocusLink	Gene	Comments
Table of Contents	Not retained
Alphabetic lists	Not retained
Gene diagram	Transcripts and Products	Gene adds the function of Genomic context, to allow a quick view of nearby genes and links to their report pages.
Link to Evidence Viewer from Gene diagram	Evidence Viewer link in Links menu	The option to first see only the diagram of the alignment is not retained.
Button Links	Links menu	On the Gene Graphic/Default display, the number of links may be greater than in LocusLink.
Title bar with links to nomenclature source.	Initial text, with link to nomenclature source via LocusTag.	Links from LocusTag values may connect to an external database where official nomenclature has not been assigned.
OVERVIEW SECTION
RefSeq Summary	Summary	not changed
Locus type	Combination of Gene type and evidence type (under development)	The text values are not equivalent. LocusLink's Locus type values are being subdivided into Gene type and Evidence type categories.
Protein names	General protein information	not changed
Alternate symbols	Gene aliases	not changed
RELATIONSHIPS SECTION
Homology data	Links menu; HomoloGene	What is printed in LocusLink is still printed in Gene.
Related models	Related	not changed; limited to genomes being annotated by NCBI's pipeline.
FUNCTION SECTION
GeneRIFS	GeneRIFs	Not in a function section; indented under Bibliography
GO annotation	General gene information: GeneOntology	organization changed, but not content
Phenotype	General gene information: Phenotypes	organization changed, but not content
MAP SECTION
Chromosome	Genomic context	not changed
Associated markers	General gene information:Sequence Tagged Site (Markers)	Entrez Gene added display of alternate marker names.
SEQUENCE SECTION
RefSeq Sub Section
Category	RefSeq status	not changed
GenBank source	Source sequence	not changed
Domain matches	Domains	CDD link also attached to the protein accession in Transcripts and Products and in Links menu.
BL (BLink)	BLink link attached to the protein accession in the Transcripts and Products section	The function was not changed, but the placement and visibility are different.
Variant name	After the protein accession in the Transcripts and Products section	content not changed
Annotation SubSection
Genomic contig	Transcripts and Products	function retained
gb: Link to gene-specific subsequence	GENBANK view from source NC, NT, or NW accession	function retained as GENBANK option from the genomic accession-based menu.
svLink to graphic display of gene-specific subsequence	GRAPHICS view from source NC, NT, or NW accession	function retained as GRAPHIC option from the genomic accession-based menu.
mv: Map Viewer	Map Viewer in Links menu	function retained
ev: Evidence viewer	Evidence Viewer in Links menu	function retained
mm: ModelMaker	ModelMaker in Links menu	function retained
strain or haplotype	not retained
Related Sequences Subsection
Accessions, type, and strain data	Related Sequences	content not changed.
BL (BLink) from protein accessions	not retained
Additional Links	Additional Links

ASN.1 Display

The ASN.1 display provides Gene records structured according to the Entrezgene specification. An XML transformation of the ASN.1 is also provided by use of Display XML. Detailed information about the specification is provided in the For the Programmer Section.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display XML

Any record or selected set of records can be displayed in XML format. The XML is generated automatically from the ASN.1 record that is used to support the display, with the names of the tags defined by the ASN.1 specification. Detailed information about the specification is provided in the For the Programmer Section.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display Gene Table

The Gene Table display reports the intron/exon organization of each transcript, and, if an mRNA, the region of each exon that contains coding sequence. (Sample) It does this in two ways:

1. graphically, by repeating the display included in the Graphic display
2. in a table, by reporting the position of any exon, intron, or coding region.

In addition to allowing you to browse the structure of any gene and it products, this view also makes it easier to view and download the gene-related sequence as summarized in the following table. Please note:

• If the gene has not [yet] been annotated on any of NCBI's Genomic RefSeqs, this function is not supported.
• The sequence being retrieved is from the indicated genomic sequence, not the RNA. That means that the length of a poly(A) tail is not included in the report.
• Whatever display format results from your selection, at the sequence-specific nucleotide or protein record, you can use the Display options there to generate the display option you prefer.

Navigation If there are multiple gene products (RNAs/proteins) annotated for a gene, navigation within the page is facilitated by the following:

• The RefSeq accessions in the first table under the graphic support jumping down to the exon report specific to that accession.
• Blue-shaded icons at the right of the RefSeq accessions repeated at the top of the exon-specific table allow you to:
  • go to the top of the page
  • go to the table for the previous product
  • go to the table for the next product

Display UI List

This display is essentially the same as that of the Brief format, with the addition of the unique identifiers for a Gene record on the second line. The difference between the Brief and UI List displays is more apparent, however, when selecting the Send to Text option. For UI List, only the Gene identifiers are reported.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalent is the Save All Loci function that provides the record as text.

Display LinkOut

The goal of the LinkOut feature is to facilitate access to relevant online resources beyond the Entrez system to extend, clarify, or supplement information found in the Entrez databases. Resources external to the Entrez system can submit their links as described here. Display LinkOut thus functions to show which records have supplemental information available from LinkOut providers and support connections to those providers.

Tips for Previous Users of LocusLink

There is no direct precedent in LocusLink. The nearest equivalents are the links integrated into the LocusLink record.

Display Book Links

An increasing number of Gene records are described in books and monographs provided in the Bookshelf. For sample records in this category, try the query "gene books"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

The Book Links correspond to the Books button displayed at the top of the LocusLink report page for records known to be linked to information in books in the Bookshelf.

Display GEO Links

When expression data are reported for sequences associated with a Gene record, a link to the Gene Expression Omnibus is provided. For sample records in this category, try the query "gene geo"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

There are no connections to GEO in LocusLink.

Display HomoloGene Links

These links are maintained by the HomoloGene staff, based on When expression data are reported for sequences associated with a Gene record, a link to the Gene Expression Omnibus is provided. For sample records in this category, try the query "gene geo"[filter] in the Gene query bar.

Tips for Previous Users of LocusLink

These links are the equivalent of the [H]omology button displayed from the Brief or Summary displays of query results and for the HOMOL button on the Locus Report page.

Display Nucleotide Links

Display OMIM Links

Display Protein Links

Display PubMed Links

Display SNP Links

Display Taxonomy Links

Display UniGene Links

Display UniSTS Links

Query tips

All functions of the Entrez indexing and query engine are used by Gene. This section will therefore summarize only how to use the tools in the context of the Gene database. General instructions for all Entrez databases are available here.

• Limits
• Preview/Index
• History
• Clipboard
• Details
• Examples
• FAQ

Limits

The limits page allows you to set the context for making queries to Entrez Gene.It is accessed from the Limits tab at the lower left in the grey query bar.

If, for example, you want to retrieve only genes encoded on plastids, you would check 'Plastids' in the Include Only section, enter your additional query terms in the Search for box, and press Go.The Limits is designed to make it easier to do the following types of queries by checking boxes, rather than writing out the text of an Entrez query. Please be reminded that Limits remain through multiple queries, unless you 'deselect' them. You can see if Limits are set on your current query result by the explicatory text in the yellow banner toward the top of the results page. You can discontinue the Limits functionality at any time by removing the check to the left of the word Limits in the query bar of a result page.

• Exclude certain genes from your result set.
  The Exclude section allows you to prevent certain types of genes from being included in your result set. Each check box is independent, so if you want to prevent retrieving both genes encoded by mitochondria and plastids, check both boxes. The NEWENTRY option refers to the GeneID used to support submission of GeneRIFs, by species, for a gene not currently in Entrez Gene. Checking All of the above prevents all in the section from being retrieved.
• Include Only certain genes in your result set.
  • Genomic: genes encoded by chromosomes or the major genomic macromolecule for the taxon.
  • Mitochondria: genes encoded by mitochondria
  • Plasmids: genes encoded by plasmids
  • Plastids: genes encoded by plastids
  • RefSeqs: for which RefSeqs exist
  • NEWENTRY records: GeneIDs used to support submission of GeneRIFs, by species, for a gene not currently in Entrez Gene.
• Limit by Refseq Status
  Retrieve genes based on the type of RefSeq used to represent the Gene.
• Limit by Taxonomy
  This set of check boxes functions to restrict the result set to the taxonomic nodes that are checked. This function to make it easier to restrict your query by organism. The limits are treated as 'Include only', and are hierarchical. So to limit your results to genes in invertebrate genomes, check 'Invertebrates'. The these selections are also treated as the boolean OR, so if you want to retrieve genes from either Danio rerio or Xenopus sp., check both Danio rerio and Xenopus.
• Field restriction This option allows you to retrieve records only when your query term exists in the selected field. These fields are the same as those described in the Preview/Index section.
• Creation date
  Retrieve records created within the range entered, or according to preselected ranges in the pull-down menu.
• Last modified
  Retrieve records modified within the range entered, or according to preselected ranges in the pull-down menu.

Examples using limits:

• retrieve non-mitochondrially encoded NADH dehydrogenases from human, mouse, or rat
  1. Use the Limits form and check human, mouse, and rat
  2. Use the Limits form and check mitochondrion under Exclude
  3. Use the Limits form to select Gene/Protein name from the All fields menu
  4. enter nadh dehydrogenase in the query box (case does not matter)
  5. Press Go.

• retrieve E. coli genes related to tryptophan
  1. Use the limits form and check Escherichia coli.
  2. enter tryptophan in the query box
  3. Press Go.

Preview/Index

The Preview/Index page on any Entrez database is a powerful resource to construct useful queries and to view terms that have been indexed under any field name. Table 4 in the previous section described the fields used in indexing the records and provided some representative queries using those fields. This section will:

1. Describe filters in general and how they can be used to find records of interest in gene.
2. Describe the properties assigned to gene records and provide examples of how to use them.

The genetype options should be self-explanatory, except perhaps for miscrna, other and unknown. Names for the types of molecules encoded by genes follow the conventions of the collaborating sequence databases (DDBJ/EMBL/GenBank); thus miscrna (misc_rna, miscellaneous RNA) is assigned to any gene that encodes an RNA product not included in the other specifics. The genetype other property is applied to loci of known type, but a specific category has not yet been applied in the Entrezgene data model (i.e.named fragile sites). The genetype unknown property is applied to probable genes for which the type is still under review. This category is frequently used when the defining sequence has uncertain coding propensity. NOTE: At the time of this writing, the assignment of gene records to the latter two categories continues to be refined. We appreciate your suggestions for any improvements.

The source options should be self-explanatory, with source other being used where a specific category has not yet been applied in the Entrezgene data model.

The srcdb refseq categories are as enumerated by RefSeq and will not be duplicated here.

The other properties (i.e #4 above) are explained in the following table.

History

Use of History in Entrez Gene is consistent with all other Entrez databases. You may refer to the History section of the Entrez help documentation for more information.

Clipboard

Use of Clipboard in Entrez Gene is consistent with all other Entrez databases. You may refer to the Clipboard section of the Entrez help documentation for more information.

Details

Use of Details in Entrez Gene is consistent with all other Entrez databases. You may refer to the Details Button section of the Entrez help documentation for more information.

Examples

Tips for the programmer

Sections under development include:

• the Gene data model
• converting from use of LL_tmpl to Entrezgene.asn for gene-specific information.
• converting from use of the LocusLink ftp site to the Entrez Gene ftp site.
• Entrez e-Utilities and Entrez gene

The Gene Data Model

The data model for Entrez gene is documented in the Entrezgene specification. It combines several definitions used by other NCBI databases, such as seqfeat, but also establishes definitions specific to Entrezgene. Of special note is the Gene-commentary, which is used to represent many descriptors of genes. Each Gene-commentary is defined by type, and supports specific representation of such elements as sequence database accessions (accession, version), citations (refs), external or internal resources defining the data (source), and position information. Heading, label, and text are used for general data, with the choice influenced by display in the Entrez Gene viewers.

Converting from Use of LL_tmpl

Entrezgene ::= {

Entrezgene ::= {
  track-info {
    geneid 2,

Entrezgene ::= {
  track-info {
    geneid 217346,
    status secondary,
    current-id {
      {
        db "LocusID",
        tag id 193217
      },
      {
        db "GeneID",
        tag id 193217
      }
    },

type protein-coding,

source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
      db {
        {
          db "taxon",
          tag id 9606
        }
      },
      syn {
        "man"
      },
      orgname {
        name binomial {
          genus "Homo",
          species "sapiens"
        },
        lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
 Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo",
        gcode 1,
        mgcode 2,
        div "PRI"
      }
    },

homology {
    {
      type comment,
      heading "Mouse",
      label "A2m",
      text "6 62.00 cM",
      source {
        {
          src {
            db "HomoloGene",
            tag str "A2m"
          },
          anchor "A2m",
          url "http://www.ncbi.nlm.nih.gov/Homology/view.cgi?map=ncbi_mgd&tax;_
id=10090&chr;=6&symbol;=A2m"
        }
      }
    }
  },

    {
      type comment,
      heading "RefSeq Status",
      label "REVIEWED"
    },

 locus {
    {
      type genomic,
      label "tat",
      accession "NC_001802",
      seqs {
        int {
          from 5376,
          to 7969,
          strand plus,
          id gi 9629357
        }
      },

   {
      type comment,
      heading "NCBI Reference Sequences (RefSeq)",
      comment {
        {
          type genomic,
          heading "Reference",
          accession "NG_002315",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 24047158
              },
              anchor "NG_002315"
            }
          },
          seqs {
            int {
              from 1,
              to 652,
              strand plus,
              id gi 24047158
            }
          }
        }
      }
    },

         products {
            {
              type peptide,
              heading "Product",
              accession "NP_000005",
              version 3,
              source {
                {
                  src {
                    db "Protein",
                    tag id 4557225
                  },
                  anchor "NP_000005",
                  post-text "alpha 2 macroglobulin precursor"
                }
              },

         comment {
            {
              type comment,
              heading "Transcriptional Variant",
              comment {
                {
                  type comment,
                  text "Transcript Variant: This variant (PAX3A) includes an
 alternate segment in the coding region, which causes a frameshift, and lacks
 several segments in the 3' coding region, compared to variant PAX3. The
 resulting protein (isoform PAX3a) has a shorter and distinct C-terminus,
 compared to isoform PAX3. Isoform PAX3a lacks the paired-type homeodomain."
                }
              }
            },

          {
              type other,
              heading "Source Sequence",
              source {
                {
                  src {
                    db "Nucleotide",
                    tag str "AJ007392,S69369"
                  },
                  anchor "AJ007392,S69369"
                }
              },

comment {
                {
                  type other,
                  heading "Domains",
                  comment {
                    {
                      type other,
                      source {
                        {
                          src {
                            db "CDD",
                            tag id 5952
                          },
                          anchor "pfam00207: Alpha-2-macroglobulin family",
                          post-text "score:2365"
                        }
                      }
                    },

     type comment,
      heading "Related Sequences",
      products {
        {
          type mRNA,
          heading "mRNA",
          accession "AY185125",
          version 1,
          source {
            {
              src {
                db "Nucleotide",
                tag id 27966960
              },
              anchor "AY185125"
            }
          },
          seqs {
            whole gi 27966960
          },
          products {
            {
              type peptide,
              accession "AAO25741",
              version 1,
              source {
                {
                  src {
                    db "Protein",
                    tag id 27966961
                  },
                  anchor "AAO25741"
                }
              },
              seqs {
                whole gi 27966961
              }
            }
          },
          comment {
            {
              type other,
              label "Strain",
              text "C57BL/6"
            }
          }
        },

gene {
    locus "A2m",
    desc "alpha-2-macroglobulin",
    ...

 gene {
    desc "spongiotrophoblast specific protein",
    maploc "17p14",
    db {
      {
        db "LocusID",
        tag id 64509
      }
    },
    syn {
      "Tpbp"
    },
    locus-tag "RGD:621454"
  },

type peptide,
              heading "Product",
              accession "NP_057236",
              version 2,
              source {
                {
                  src {
                    db "Protein",
                    tag id 7706625
                  },
                  anchor "NP_057236",
                  post-text "retinoic acid receptor, beta isoform 2"
                }
              },
              seqs {
                whole gi 7706625
              },

  syn {
      "HAP",
      "RRB2",
      "NR1B2"
    },

  prot {
    name {
      "retinoic acid receptor, beta",
      "RAR-epsilon",
      "RAR, beta form",
      "HBV-activated protein",
      "retinoic acid receptor beta 2",
      "retinoic acid receptor beta 4",
      "hepatitis B virus activated protein",
      "retinoic acid receptor, beta polypeptide"
    }
  },

      type comment,
      heading "Phenotypes",
      comment {
        {
          type comment,
          text "Cystic fibrosis",
          source {
            {
              src {
                db "MIM",
                tag id 219700
              },
              anchor "MIM: 219700"
            }
          }
        },
        {
          type comment,
          text "Pancreatitis, idiopathic",
          source {
            {
              src {
                db "MIM",
                tag id 602421
              },
              anchor "MIM: 602421"
            }
          }
        },
        {
          type comment,
          text "Sweat chloride elevation without CF",
          source {
            {
              src {
                db "MIM",
                tag id 602421
              },
              anchor "MIM: 602421"
            }
          }
        }
      }
    },

{
      type comment,
      heading "Additional Links",
      comment {
        {
          type comment,
          text "UniGene",
          source {
            {
              src {
                db "UniGene",
                tag str "Hs.411882"
              },
              anchor "Hs.411882",
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID;=41
1882"
            }
          }
        },

{
      type comment,
      heading "Additional Links",
      ...
      comment {
          type comment,
          text "MIM",
          source {
            {
              src {
                db "MIM",
                tag str "602421"
              },
              anchor "602421"
            }
          }
        },

  
source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
    ...
    },
    subtype {
      {
        subtype chromosome,
        name "7"
    ...

  location {
    {
      display-str "7q31.2",
      method map-type cyto
    }
  },

 {
      type comment,
      heading "Sequence Tagged Site (Markers)",
      comment {
        {
          type comment,
          source {
            {
              src {
                db "UniSTS",
                tag id 12967
              },
              anchor "D7S2742",
              post-text "(e-PCR)"
            }
          },
          comment {
            {
              type other,
              label "Alternate name",
              text "G00-674-897"
            },
            {
              type other,
              label "Alternate name",
              text "G11318"
            },
            {
              type other,
              label "Alternate name",
              text "G13271"
            },
     ...

              comment {
                {
                  type property,
                  label "EC",
                  text "1.2.3.1"
                }
              }

      
type comment,
      heading "Additional Links",
      comment {
        {
          type comment,
          text "UniGene",
          xtra-properties {
            {
              tag "UNIGENE",
              value "Hs.74561"
            }
          },
          source {
            {
              src {
                db "UniGene",
                tag str "Hs.74561"
              },
              anchor "Hs.74561",
              url "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID;=74
561"
            }
          }
        },

 {
      type comment,
      refs {
        pmid 14637088,
        pmid 14506912,
        pmid 1370808,
        pmid 1281457
      }
    },

  properties {
    {
      type comment,
      heading "GeneOntology",
      source {
        {
          pre-text "Provided by",
          anchor "RGD",
          url "http://rgd.mcw.edu/"
        }
      },
      comment {
        {
          type comment,
          label "Function",
          comment {
            {
              type comment,
              source {
                {
                  src {
                    db "GO",
                    tag id 3677
                  },
                  anchor "DNA binding",
                  post-text "evidence: IEA"
                }
              }
            }
          }
        },

Entrez Gene ftp site

Connect here

• DATA

• GeneRIF

• nomenclature (gene_info.gz)
• associated RefSeq accessions (gene2refseq.gz) and
• citations (gene2pubmed.gz).

• the GeneRIF pipeline (generifs_basic.gz) or
• the HIV-1, Human Protein Interaction Database (hiv_interactions.gz).

The tab-delimited files are not subdivided by species of interest. bAll files except the file reporting GeneID / PubMedID relationships (gene2pubmed.gz) have a column with the ID from the NCBI taxonomy database, to facilitate extracting a subset of the data from the file by species.

Entrez e-Utilities and Gene

Under development