SGD Help: Systematic Names - Protein Coding ORFs

Contents

Description
Background On ORF Systematic Names
Assigning Systematic Names To New ORFs

Description

This page describes how the systematic names of protein coding genes were assigned, and how systematic names of newly discovered protein coding ORFs are determined. Please note that new ORFs are assigned systematic names by SGD and MIPS. If you have discovered a new ORF, please contact SGD in order to have the proper systematic name assigned.

If you would like information on the systematic names of other types of genes (tRNAs, snoRNAs, ARSes, etc.), please see the Gene Nomenclature Conventions help page.

Background On ORF Systematic Names

When the S. cerevisiae genome was completed in 1996, each predicted protein coding ORF was assigned a unique systematic name that indicated the relative chromosomal postion of that ORF. In this original assignment of systematic names, ORFs were numbered from the centromere to the telomere, regardless of which strand they were on. The figure below shows the base name of some hypothetical ORFs: the "Y" means "Yeast"; the "X" indicates the chromosome number (A=1, B=2, etc.); the "L" or "R" indicates the position relative to the centromere (Left or Right).
ORFs also have a suffix, indicated in green below, to indicate which strand the ORF is on. "W" = "Watson" = top strand; "C" = "Crick" = bottom strand

Assigning Systematic Names To New ORFs

Many new ORFs have been discovered since the original assignment of systematic names.

New ORFs are assigned systematic names by SGD and MIPS. If you have discovered a new ORF, please contact SGD in order to have the proper systematic name assigned. SGD and MIPS use the following steps to determine the correct systematic name. As in the original assignments, new ORFs are numbered from the centromere to the telomere, regardless of strandedness.
1. The base name of the new ORF is the same as the closest centromere proximal ORF. The correct base names for the example new ORFs are in green below. Note that the closest centromere proximal ORF does not have to be on the same strand, although it can be. The new ORF may overlap an existing ORF. When this occurs, if any portion of the existing overlapping ORF is closer to the centromere than the new ORF, then the existing overlapping ORF is "centromere proximal" relative to the new ORF.
2. The W/C suffix indicates the strandedness of the new ORF. The W/C suffix of the new ORF is independent of the strandedness of the centromere proximal ORF. The correct suffixes for the example new ORFs are in green below.
3. An additional suffix, -[letter], is appended to the name of the new ORF. This distinguishes the new ORF from ORFs named in the original annotation. The letters are assigned in alphabetical order, per base name, in order of discovery (see additional examples below). The correct suffixes for the example new ORFs are in green below. If several neighboring new ORFs are added simultaneously, then the -[letter] suffix is assigned in alphabetical order, from the centromere to the telomere. However, since new neighboring new ORFs are not necessarily discovered simultaneously, the -[letter] suffix does not always indicate relative position.
Some more examples, indicated in green. It is very important to remember that strandedness does not matter when determining the correct base name or -[letter] suffix. For example, "YXL002W" and "YXL002C" have the same base name (YXL002), even though they are are on different strands. Since these new ORFs have the same base name, they must have different -[letter] suffixes.
In the rare event that a new ORF is discovered at the extreme end of a chromosome, the new ORF is given the next number in the sequence and does not require a -[letter] suffix. This is only applicable in cases where that there are no existing ORFs between the new ORF and the end of the chromosome.

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