StATS: Naming conventions for genes, proteins, etc. (September 8, 2005).

When you are analyzing a microarray experiment, the mRNA sequences can be referred to by several different names.

Affymettrix IDs

Clone ID

EC (Enzyme Commission) numbers

GenBank Accession Numbers

The GenBank Accession numbers are one or two upper case letters followed by five or six numeric digits.

GO (Gene Ontology) terms or identifiers

Gene Symbols

Locus Name

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. www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

LocusLink ID

RefSeq Accession Numbers

The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms. RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. www.ncbi.nlm.nih.gov/RefSeq/index.html

SwissProt/UniProt

These are six characters long where the first character is either O, P, or Q, the second and sixth characters are numeric digits, and the remaining characters are either upper case letters or numeric digits.

The purpose of accession numbers is to provide a stable way of identifying entries from release to release. It is sometimes necessary for reasons of consistency to change the names of the entries, for example, to ensure that related entries have similar names. However, an accession number is always conserved, and therefore allows unambiguous citation of entries. Researchers who wish to cite entries in their publications should always cite the first accession number. This is commonly referred to as the 'primary accession number'. 'Secondary accession numbers' are sorted alphanumerically. We strongly advise those users who have programs performing mappings of Swiss-Prot to another data resource to use Swiss-Prot accession numbers to identify an entry. Entries will have more than one accession number if they have been merged or split. For example, when two entries are merged into one, the accession numbers from both entries are stored in the AC line(s). If an existing entry is split into two or more entries (a rare occurrence), the original accession numbers are retained in all the derived entries and a new primary accession number is added to all the entries. An accession number is dropped only when the data to which it was assigned have been completely removed from the database. Accession numbers deleted from Swiss-Prot are listed in the document file delac_sp.txt and those deleted from TrEMBL are listed in delac_tr.txt. ca.expasy.org/sprot/userman.html#AC_line

Other information

The AC (ACcession number) line lists the accession numbers associated with the entry. Examples of accession number lines are shown below:

AC X56734; S46826;
AC Y00001; X00001-X00005; X00008; Z00001-Z00005;

Each accession number, or range of accession numbers, is terminated by a semicolon. Where necessary, more than one AC line is used. Consecutive secondary accession numbers in EMBL database flatfiles are shown in the form of inclusive accession number ranges.

Accession numbers are the primary means of identifying sequences providing a stable way of identifying entries from release to release. An accession number, however, always remains in the accession number list of the latest version of the entry in which it first appeared. Accession numbers allow unambiguous citation of database entries. Researchers who wish to cite entries in their publications should always cite the first accession number in the list (the "primary" accession number) to ensure that readers can find the relevant data in a subsequent release. Readers wishing to find the data thus cited must look at all the accession numbers in each entry's list.

Secondary accession numbers: One reason for allowing the existence of several accession numbers is to allow tracking of data when entries are merged or split. For example, when two entries are merged into one, a "primary" accession number goes at the start of the list, and those from the merged entries are added after this one as "secondary" numbers. Example: AC X56734; S46826; Similarly, if an existing entry is split into two or more entries (a rare occurrence), the original accession number list is retained in all the derived entries. An accession number is dropped from the database only when the data to which it was assigned have been completely removed from the database. www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html

Further reading:

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