Sort the following features based on whether they apply to DNA or RNA

This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can see the corresponding live record for U49845, and see examples of other records that show a range of biological features.

LOCUS

The LOCUS field contains a number of different data elements, including locus name, sequence length, molecule type, GenBank division, and modification date. Each element is described below.

Locus Name

The locus name in this example is SCU49845.

The locus name was originally designed to help group entries with similar sequences: the first three characters usually designated the organism; the fourth and fifth characters were used to show other group designations, such as gene product; for segmented entries, the last character was one of a series of sequential integers. (See GenBank release notes section 3.4.4 for more info.)

However, the 10 characters in the locus name are no longer sufficient to represent the amount of information originally intended to be contained in the locus name. The only rule now applied in assigning a locus name is that it must be unique. For example, for GenBank records that have 6-character accessions (e.g., U12345), the locus name is usually the first letter of the genus and species names, followed by the accession number. For 8-character character accessions (e.g., AF123456), the locus name is just the accession number.

The RefSeq database of reference sequences assigns formal locus names to each record, based on gene symbol. RefSeq is separate from the GenBank database, but contains cross-references to corresponding GenBank records.

Entrez Search Field: Accession Number [ACCN] Search Tip : It is better to search for the actual accession number rather than the locus name, because the accessions are stable and locus names can change.

Sequence Length

Number of nucleotide base pairs (or amino acid residues) in the sequence record. In this example, the sequence length is 5028 bp.

Entrez Search Field : Sequence Length [SLEN] Search Tips : (1) To retrieve records within a range of lengths, use the colon as the range operator, e.g., 2500:2600[SLEN]. (2) To retrieve all sequences shorter than a certain number, use 2 as the lower bound, e.g., 2:100[SLEN]. (3) To retrieve all sequences longer than a certain number, use a series of 9's as the upper bound, e.g., 325000:99999999[SLEN].

Molecule Type

The type of molecule that was sequenced. In this example, the molecule type is DNA.

Each GenBank record must contain contiguous sequence data from a single molecule type. The various molecule types can include genomic DNA, genomic RNA, precursor RNA, mRNA (cDNA), ribosomal RNA, transfer RNA, small nuclear RNA, and small cytoplasmic RNA.

Entrez Search Field : Properties [PROP] Search Tip : Search term should be in the format: biomol_genomic, biomol_mRNA, etc. For more examples, view the Properties field in the Index mode.

GenBank Division

The GenBank division to which a record belongs is indicated with a three letter abbreviation. In this example, GenBank division is PLN.

The GenBank database is divided into 18 divisions:

1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
10. SYN - synthetic sequences
11. UNA - unannotated sequences
12. EST - EST sequences (expressed sequence tags)
13. PAT - patent sequences
14. STS - STS sequences (sequence tagged sites)
15. GSS - GSS sequences (genome survey sequences)
16. HTG - HTG sequences (high-throughput genomic sequences)
17. HTC - unfinished high-throughput cDNA sequencing
18. ENV - environmental sampling sequences

Some of the divisions contain sequences from specific groups of organisms, whereas others (EST, GSS, HTG, etc.) contain data generated by specific sequencing technologies from many different organisms. The organismal divisions are historical and do not reflect the current NCBI Taxonomy. Instead, they merely serve as a convenient way to divide GenBank into smaller pieces for those who want to FTP the database. Because of this, and because sequences from a particular organism can exist in technology-based divisions such as EST, HTG, etc., the NCBI Taxonomy Browser should be used for retrieving all sequences from a particular organism.

Entrez Search Field : Properties [PROP] Search Tip : Search term should be in the format: gbdiv_pri, gbdiv_est, etc. For more examples, view the Properties field in the Index mode. For example, to eliminate all sequences from a particular division, such as all ESTs, you can use a Boolean query formatted such as: human[ORGN] NOT gbdiv_est[PROP] For the reasons noted above, do not use GenBank divisions to retrieve all sequences from a specific organism. Instead, use the NCBI Taxonomy Browser.

The date in the LOCUS field is the date of last modification. The sample record shown here was last modified on 21-JUN-1999.

Entrez Search Field : Modification Date [MDAT] Search Tips : (1) Enter search term in the format: yyyy/mm/dd, e.g., 1999/07/25. (2) To retrieve records modified between two dates, use the colon as a range operator, e.g., 1999/07/25:1999/07/31[MDAT]. (3) You can use the Publication Date [PDAT] field of Entrez to limit search results by the date on which records were added to the Entrez system. Publication date can be in the form of a range, just like the Modification Date.

DEFINITION

Brief description of sequence; includes information such as source organism, gene name/protein name, or some description of the sequence's function (if the sequence is non-coding). If the sequence has a coding region (CDS), description may be followed by a completeness qualifier, such as "complete cds".

Entrez Search Field: Title Word [TITL] Search Tip : Although nucleotide definition lines follow a structured format, GenBank does not use a controlled vocabulary, and authors determine the content of their records. Therefore, if a search for a specific term does not retrieve the desired records, try other terms that authors might have used, such as synonyms, full spellings, or abbreviations. The "related records" (or "neighbors") function of Entrez also allows you to broaden your search by retrieving records with similar sequences, regardless of the descriptive terms used by the submitters.

ACCESSION

The unique identifier for a sequence record. An accession number applies to the complete record and is usually a combination of a letter(s) and numbers, such as a single letter followed by five digits (e.g., U12345) or two letters followed by six digits (e.g., AF123456). Some accessions might be longer, depending on the type of sequence record.

Accession numbers do not change, even if information in the record is changed at the author's request. Sometimes, however, an original accession number might become secondary to a newer accession number, if the authors make a new submission that combines previous sequences, or if for some reason a new submission supercedes an earlier record.

Records from the RefSeq database of reference sequences have a their own accession number format that begins with two letters followed by an underscore bar and six or more digits; for example:

Note: Most records have both a series of accession numbers (Version for nucleotide sequences and protein_id for amino acid sequences) and sequence identifiers (GI for nucleotide sequences and GI for amino acid sequences). See the online documentation for Sequence IDs for details.

Entrez Search Field: Accession [ACCN] Search Tip : The letters in the accession number can be written in upper- or lowercase. RefSeq accessions must contain an underscore bar between the letters and the numbers, e.g., NM_002111.

VERSION

A nucleotide sequence identification number that represents a single, specific sequence in the GenBank database. This identification number uses the accession.version format implemented by GenBank/ENA/DDBJ in February 1999.

If there is any change to the sequence data (even a single base), the version number will be increased, e.g., U12345.1 ? U12345.2, but the accession portion will remain stable.

The accession.version system of sequence identifiers runs parallel to the GI number system--when any change is made to a sequence, it receives a new GI number AND its version number is incremented by one.

To find out about the revision history of a sequence, see GenBank Sequence Revision History.

Entrez Search Field: use the default setting of "All Fields"

GI

"GenInfo Identifier" sequence identification number, in this case, for the nucleotide sequence. If a sequence changes in any way, a new GI number will be assigned.

A separate GI number is also assigned to each protein translation within a nucleotide sequence record, and a new GI is assigned if the protein translation changes in any way (see below).

GI sequence identifiers run parallel to the new accession.version system of sequence identifiers.

Read more about GenBank Sequence Revision History and Sequence IDs.

Entrez Search Field: use the default setting of "All Fields"

KEYWORDS

Word or phrase describing the sequence. If no keywords are included in the entry, the field contains only a period.

The Keywords field is present in sequence records primarily for historical reasons, and is not based on a controlled vocabulary. Keywords are generally present in older records. They are not included in newer records unless the record contains a special type of sequence such as EST, STS, GSS, HTG, etc.

Entrez Search Field: Keyword [KYWD] Search Tip : Because keywords are not present in many records, it is best not to search that field. Instead, search All Fields [ALL], the Text Word [WORD] field, or the Title Word [TITL] field, for progressively narrower retrieval.

SOURCE

Free-format information including an abbreviated form of the organism name, sometimes followed by a molecule type.

Entrez Search Field: Organism [ORGN] Search Tip : For some organisms that have well-established common names, such as baker's yeast, mouse, and human, a search for the common name will yield the same results as a search for the scientific name, e.g., a search for "baker's yeast" in the organism field retrieves the same number of documents as "Saccharomyces cerevisiae". This is true because the Organism field is connected to the NCBI Taxonomy Database, which contains cross-references between common names, scientific names, and synonyms for organisms represented in the Sequence databases.

Organism

The formal scientific name for the source organism (genus and species, where appropriate) and its lineage, based on the phylogenetic classification scheme used in the NCBI Taxonomy Database . If the complete lineage of an organism is very long, an abbreviated lineage will be shown in the GenBank record and the complete lineage will be available in the Taxonomy Database. (See also the /db_xref=taxon:nnnn Feature qualifer, below.)

Entrez Search Field: Organism [ORGN] Search Tip : You can search the Organism field by any node in the taxonomic hierarchy, e.g., you can search for the term "Saccharomyces cerevisiae", "Saccharomycetales", "Ascomycota", etc. to retrieve all the sequences from organisms in a particular taxon.

REFERENCE

Publications by the authors of the sequence that discuss the data reported in the record. References are automatically sorted within the record based on date of publication, showing the oldest references first.

Some sequences have not been reported in papers and show a status of "unpublished" or "in press". When an accession number and/or sequence data has appeared in print, sequence authors should send the complete citation of the article to and the GenBank staff will revise the record.

Various classes of publication can be present in the References field, including journal article, book chapter, book, thesis/monograph, proceedings chapter, proceedings from a meeting, and patent.

The last citation in the REFERENCE field usually contains information about the submitter of the sequence, rather than a literature citation. It is therefore called the "submitter block" and shows the words "Direct Submission" instead of an article title. Additional information is provided below, under the header Direct Submission. Some older records do not contain a submitter block.

Entrez Search Field: The various subfields under References are searchable in the Entrez search fields noted below.

List of authors in the order in which they appear in the cited article.

Entrez Search Field: Author [AUTH] Search Tip : Enter author names in the form: Lastname AB (without periods after the initials). Initials can be omitted. Truncation can also be used to retrieve all names that begin with a character string, e.g., Richards* or Boguski M*.

TITLE

Title of the published work or tentative title of an unpublished work.

Sometimes the words "Direct Submission" instead of an article title. This is usually true for the last citation in the REFERENCE field because it tends to contain information about the submitter of the sequence, rather than a literature citation. The last citation is therefore called the "submitter block". Additional information is provided below, under the header Direct Submission. Some older records do not contain a submitter block.

Entrez Search Field: Text Word [WORD] Note: For sequence records, the Title Word [TITL] field of Entrez searches the Definition Line, not the titles of references listed in the record. Therefore, use the Text Word field to search the titles of references (and other text-containing fields). Search Tip : If a search for a specific term does not retrieve the desired records, try other terms that authors might have used, such synonyms, full spellings, or abbreviations. The 'related records' (or 'neighbors') function of Entrez also allows you to broaden your search by retrieving records with similar sequences, regardless of the descriptive terms used by the submitters.

JOURNAL

MEDLINE abbreviation of the journal name. (Full spellings can be obtained from the Entrez Journals Database.)

Entrez Search Field: Journal Name [JOUR] Search Tip : Journal names can be entered as either the full spelling or the MEDLINE abbreviation. You can search the Journal Name field in the Index mode to see the index for that field, and to select one or more journal names for inclusion in your search.

PUBMED

PubMed Identifier (PMID).

References that include PubMed IDs contain links from the sequence record to the corresponding PubMed record. Conversely, PubMed records that contain accession number(s) in the SI (secondary source identifier) field contain links back to the sequence record(s).

Entrez Search Field: It is not possible to search the Nucleotide or Protein sequence databases by PubMed ID. However, you can search the PubMed (literature) database of Entrez for the PubMed ID, and then link to the associated sequence records.

Contact information of the submitter, such as institute/department and postal address. This is always the last citation in the References field. Some older records do not contain the "Direct Submission" reference. However, it is required in all new records.

The Authors subfield contains the submitter name(s), Title contains the words "Direct Submission", and Journal contains the address.

The date in the Journal subfield is the date on which the author prepared the submission. In many cases, it is also the date on which the sequence was received by the GenBank staff, but it is not the date of first public release.

Entrez Search Field: Use the Author Field [AUTH] if searching for the author name. Use All Fields [ALL] if searching for an element of the author's address (e.g., Yale University). Note, however, that retrieved records might contain the institution name in a field such as Comment, rather than in the Direct Submission reference, so you might get some false hits. Search Tip : It is sometimes helpful to search for both the full spelling and an abbreviation, e.g., "Washington University" OR "WashU", because the spelling used by authors might vary.

FEATURES

Information about genes and gene products, as well as regions of biological significance reported in the sequence. These can include regions of the sequence that code for proteins and RNA molecules, as well as a number of other features.

A complete list of features is available in the following places:

The location of each feature is provided as well, and can be a single base, a contiguous span of bases, a joining of sequence spans, and other representations. If a feature is located on the complementary strand, the word "complement" will appear before the base span. If the " < " symbol precedes a base span, the sequence is partial on the 5' end (e.g., CDS <1..206). If the ">" symbol follows a base span, the sequence is partial on the 3' end (e.g., CDS 435..915>).

The sample record shown here only includes a small number of features (source, CDS, and gene, all of which are described below). The Other Features section, below, provides links to some GenBank records that show a variety of additional features.

Entrez Search Field: Feature Key [FKEY] Search Tip : To scroll through the list of available features, view the Feature Key field in Index mode. You can then select one or more features from the index to include in your query. For example, you can limit your search to records that contain both primer_bind and promoter features.

source

Mandatory feature in each record that summarizes the length of the sequence, scientific name of the source organism, and Taxon ID number. Can also include other information such as map location, strain, clone, tissue type, etc., if provided by submitter.

Entrez Search Field: All Fields [ALL] can be used to search for some elements in the source field, such as strain, clone, tissue type.

Use the Sequence Length [SLEN] field to search by length and the Organism [ORGN] field to search by organism name.

Because map location is written as free text and can be represented in a number of ways (e.g., chromosome number, cytogenetic location, marker name, physical map location), it is not directly searchable in the Entrez Nucleotide or Protein databases. However, there are a number of resources that allow you to browse and/or search the maps of various genomes.

Taxon

A stable unique identification number for the taxon of the source oganism. A taxonomy ID number is assigned to each taxon (species, genus, family, etc.) in the NCBI Taxonomy Database. See also the Organism field, above.

Entrez Search Field: The Taxonomy ID number is not searchable in the Organism search field of Entrez but is searchable in the Taxonomy Browser.

Note: The /db_xref qualifier is one of many that can be applied to various features. A complete list is available in Appendix IV: Summary of qualifiers for feature keys of the DDBJ/EMBL/GenBank Feature Table, and in section 3.4.12.3 of the GenBank release notes. Appendix III: Feature keys reference shows which qualifiers can be used with specific features (see alphabetical list).

CDS

Coding sequence; region of nucleotides that corresponds with the sequence of amino acids in a protein (location includes start and stop codons). The CDS feature includes an amino acid translation. Authors can specify the nature of the CDS by using the qualifier "/evidence=experimental" or "/evidence=not_experimental".

Submitters are also encouraged to annotate the mRNA feature, which includes the 5' untranslated region (5'UTR), coding sequences (CDS, exon), and 3' untranslated region (3'UTR).

Entrez Search Field: Feature Key [FKEY] Search Tip : You can use this field to limit your search to records that contain a particular feature, such as CDS. To scroll through the list of available features, view the Feature Key field in Index mode. A complete list of features is also available from the resources noted above.

<1..206

Base span of the biological feature indicated to the left, in this case, a CDS feature. (The CDS feature is described above, and its base span includes the start and stop codons.) Features can be complete, partial on the 5' end, partial on the 3' end, and/or on the complementary strand. Examples:

1. A complete feature is simply written as n..m. Example: 687..3158 The feature extends from base 687 through base 3158 in the sequence shown

2. The < symbol indicates partial on the 5' end. Example: <1..206. The feature extends from base 1 through base 206 in the sequence shown, and is partial on the 5' end

3. The > symbol indicates partial on the 3' end. Example: 4821..>5028. The feature extends from base 4821 through base 5028 and is partial on the 3' end.

4. complement(range) indicates that the feature is on the complementary strand. Example: complement(3300..4037). The feature extends from base 3300 through base 4037 but is actually on the complementary strand. It is therefore read in the opposite direction on the reverse complement sequence. (For an example, see the third CDS feature in the sample record shown on this page. In this case, the amino acid translation is generated by taking the reverse complement of bases 3300 to 4037 and reading that reverse complement sequence in its 5' to 3' direction.)

protein_id

A protein sequence identification number, similar to the Version number of a nucleotide sequence. Protein IDs consist of three letters followed by five digits, a dot, and a version number. If there is any change to the sequence data (even a single amino acid), the version number will be increased, but the accession portion will remain stable (e.g., AAA98665.1 will change to AAA98665.2).

The accession.version format of protein sequence identification numbers was implemented by GenBank/ENA/DDBJ in February 1999 and runs parallel to the GI number system. More details about sequence identification numbers and the difference between GI number and version are provided in Sequence Identifiers: A Historical Note.

Entrez Search Field: use the default setting of "All Fields"

GI

"GenInfo Identifier" sequence identification number, in this case, for the protein translation.

The GI system of sequence identifiers runs parallel to the accession.version system, which was implemented by GenBank, EMBL, and DDBJ in February 1999. Therefore, if the protein sequence changes in any way, it will receive a new GI number, and the suffix of the protein_id will be incremented by one..

More details about sequence identification numbers and the difference between GI number and version are provided in Sequence IDs.

Entrez Search Field: use the default setting of "All Fields"

translation

The amino acid translation corresponding to the nucleotide coding sequence (CDS). In many cases, the translations are conceptual. Note that authors can indicate whether the CDS is based on experimental or non-experimental evidence.

Entrez Search Field: It is not possible to search the translation subfield using Entrez. If you want use a string of amino acids as a query to retrieve similar protein sequences, use BLAST instead.

gene

A region of biological interest identified as a gene and for which a name has been assigned. The base span for the gene feature is dependent on the furthest 5' and 3' features. Additional examples of records that show the relationship between gene features and other features such as mRNA and CDS are AF165912 and AF090832.

Entrez Search Field: Feature Key [FKEY] Search Tip : You can use this field to limit your search to records that contain a particular feature, such as a gene. To scroll through the list of available features, view the Feature Key field in Index mode. A complete list of features is also available from the resources noted above.

complement

Indicates that the feature is located on the complementary strand.

Other Features

Examples of other records that show a variety of biological features; a graphic format is also available for each sequence record and visually represents the annotated features:

• AF165912 (gene, promoter, TATA signal, mRNA, 5'UTR, CDS, 3'UTR)
• AF090832 (protein bind, gene, 5'UTR, mRNA, CDS, 3'UTR)
• L00727 (alternatively spliced mRNAs)

A complete list of features is available from the resources noted above.

ORIGIN

The ORIGIN may be left blank, may appear as "Unreported," or may give a local pointer to the sequence start, usually involving an experimentally determined restriction cleavage site or the genetic locus (if available). This information is present only in older records.

The sequence data begin on the line immediately below ORIGIN. To view or download the sequence data in FASTA format, append ?format=fasta to the record's URL; for example, /nucleotide/U49845?format=fasta&report=text.