Topic Page for Y-genes of Escherichia coli K-12

This page has been reconstructed based on old notes and a copy of the y-name map; some elements were retrieved from the Internet Archive. Minor changes were made to reflect the current annotation count and the status of EcoCyc as the current submitter of record for the GenBank entry. Thank you to Kenn Rudd for his years of work on EcoGene.


There are currently 1336 intact y-genes and 91 y-pseudogenes with y-gene names as their primary names for a total of 1427. The y-gene systematic gene naming system is described in Rudd (1998).


The y-gene nomenclature assigns temporary systematic y-names to genes of unknown function. Once a y-gene or gene product is functionally characterized in vivo or in vitro in a significant way, it is strongly suggested that a mnemonic gene name be assigned to replace the y-name.

A search of the gene names in EcoCyc can help determine if the new name has been used. A current three-letter gene name or the first three letters of a current four letter gene name cannot be used again; re-use of synonyms is also discouraged. Common dictionary words should not be used as gene names since they are weak search terms. Personal initials or anything other than a scientific mnemonic is strongly discouraged as a gene name.

Graphic y-gene naming guide.

A map depicting the system for assigning y-gene names based on 10 centisome map intervals assigned second letters a-j and then 1 minute map sub-intervals for the third letter as a-j. Once 24 y-gene names have been assigned in any one 1 centisome map interval, a second round of letters is used in the second position of the y-gene name, e.g. after yaaZ, the next y-gene in centisome is assigned ykaA. The same thing happens in the second centisome map interval, and so on, e.g. after yabZ comes ykbA. No y-gene names should be assigned without consulting to avoid conflicts.

Y-gene Naming Code Map

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