Changes to Systematic Names

In recent years many new ORFs have been annotated in the Saccharomyce cerevisiae systematic sequence. These new ORFs were assigned systematic names by SGD and/or the Munich Information Center for Protein Sequences (MIPS). New systematic names are assigned by following the naming guidelines, with consideration of publication records.

In February 2005, it was brought to our attention that SGD and MIPS had some inconsistencies in the systematic names assigned some of these new ORFs. Curators at SGD and MIPS discussed each instance of a naming conflict and agreed upon a solution. In most cases, either MIPS or SGD changed to the systematic name used by the other database. In some cases, we chose to use a different name altogether, and the systematic name was changed at both databases. All names that have been used in either database will remain associated with the appropriate ORFs, either as systematic names or as aliases. Please note that the SGDID, chromosomal coordinates, and sequence of all of these ORFs remains unchanged.

Please do not hesitate to contact SGD curators if you have any questions about these systematic name changes, or need further clarification.

The ORFs with systematic name conflicts are listed below, arranged by chromosome. You can skip to listing for a specific chromosome by using the toolbar at the top of the table. If the chromosome is not hyperlinked in the toolbar, then there are no systematic name changes on that chromosome. Cases where the systematic name was changed at SGD are highlighted in yellow.

Chr 1 | Chr 2 | Chr 3 | Chr 4 | Chr 5 | Chr 6 | Chr 7 | Chr 8 | Chr 9 | Chr 10 | Chr 11 | Chr 12 | Chr 13 | Chr 14 | Chr 15 | Chr 16 |

Systematic name SGDID Change at SGD Date of change Comments

Previous
SGD name Previous
MIPS name Current

Chromosome 2

YBL039W-A YBL039W-B YBL039W-B S000028517 Change Systematic Name 2005-03-30 "YBL039W-A" was published in Brachat S, et al. (2003) Genome Biol 4(7):R45. This name was incorrect because there was already an ORF named YBL039C-A, and new systematic names are assigned without regard to strandedness. YBL039C-A was published in Oshiro G, et al. (2002) Genome Res 12(8):1210-20.

YBL101W-B TY2B_B YBL100W-B S000002149 Change Systematic Name;

Add MIPS Alias 2005-03-29 "YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.

YBL101W-A TY2A_B YBL100W-A S000002148 Change Systematic Name;

Add MIPS Alias 2005-03-29 "YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.

YBL101W-C YBL100W-C YBL100W-C S000028598 Change Systematic Name 2005-03-29 "YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.

Chromosome 3

YCL012C YCL011C-A YCL012C S000029705 Add MIPS Alias 2005-03-24 The systematic name YCL011C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YCL012C. Although the name "YCL012C" was in conflict with a previously described but deleted ORF (YCL012W), it was agreed to keep the "YCL012C" name because it has been published in Zhang Z and Dietrich FS (2003) Yeast 20(8):731-8

Chromosome 4

YDL159W-A YDL159W-B YDL159W-A S000007599 Add MIPS Alias 2005-03-24 The systematic name YDL159W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YDL159W-A. YDL159W-A" was published in Blandin G, et al. (2000) FEBS Lett 487(1):31-6.

YDL159C-B YDL159C-A YDL159C-B S000028612 Add MIPS Alias 2005-03-24 The systematic name YDL159C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YDL159C-B. YDL159C-B was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63.

YDR524W-A YDR524W-C YDR524W-C S000028740 Change Systematic Name 2005-03-28 "YDR524C-A" was published in Kumar et al. (2002). This name was incorrect because there was already an ORF named YDR524W-A, and new systematic names are assigned without regard to strandedness. However, the name YDR524W-A name has not been published, so it was agreed to keep the single published name and change YDR524W-A to YDR524W-C.

Chromosome 6

YFL031C-A YFL030C-A YFL031C-A S000028629 Add MIPS Alias 2005-03-24 "YFL030C-A" was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63. This name was incorrect, because YFL030W is not the cetromere proximal ORF. The centromere proximal ORF is the overlapping ORF, YFL031W. The endpoint of YFL031W is closer to the centromere than is the endpoint of the new ORF, so the new ORF should be assigned the "YFL031" base name.

Chromosome 7

YGR169C-A YGR169C-C YGR169C-A S000028521 Add MIPS Alias 2005-03-24 The systematic name YGR169C-C was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YGR169C-A. YGR169C-A was published in Brachat S, et al. (2003) Genome Biol 4(7):R45.

Chromosome 10

YJL127C-B YJL127C-A YJL127C-B S000028522 Add MIPS Alias 2005-03-24 The systematic name YJL127C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YJL127C-B. YJL127C-B was published in Brachat S, et al. (2003)Genome Biol 4(7):R45.

YJL127W-A YJL127W-B YJL127W-A S000007612 Add MIPS Alias 2005-03-24 The systematic name YJL127W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YJL127W-A. YJL127W-A was published in Blandin G, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487(1):31-6.

YJL205C YJL205C-A YJL205C S000003742 Add MIPS Alias 2003-04-02 YJL205C-A used to be the systematic name for this ORF. However, since this name was incorrectly named, this ORF name has been changed to YJL205C to properly represent the systematic ORF nomenclature. YJL205C-A is now an alias of YJL205C.

Chromosome 12

YLR154W-C YLR154W-A YLR154W-A S000028675 Change Systematic Name 2005-04-01 Neither "YLR154W-A" or "YLR154W-C" have been published. Both ORFs were described in Kumar et al. (2002) Nat Biotechnol 20(1):58-63 and in Kessler MM, et al. (2003) Genome Res 13(2):264-71, but neither of these groups assigned systematic names. A careful characterization of the ORF at 452439-452624 was published in Coelho P, et al. (2002) Genes Dev 16(21):2755-60. However, these authors also did not assign a systematic name, but simply referred to the ORF by a gene name, TAR1. SGD added the ORF described by Coelho P, et al. without realizing that it had been described earlier, in context of two other new ORFs that were located immediately downstream (closer to the centromere). As a result, both YLR154W-C and YLR154W-A needed to be changed.

YLR154W-A YLR154W-C YLR154W-C S000028422 Change Systematic Name 2005-04-01 Neither "YLR154W-A" or "YLR154W-C" have been published. Both ORFs were described in Kumar et al. (2002) Nat Biotechnol 20(1):58-63 and in Kessler MM, et al. (2003) Genome Res 13(2):264-71, but neither of these groups assigned systematic names. A careful characterization of the ORF at 452439-452624 was published in Coelho P, et al. (2002) Genes Dev 16(21):2755-60. However, these authors also did not assign a systematic name, but simply referred to the ORF by a gene name, TAR1. SGD added the ORF described by Coelho P, et al. without realizing that it had been described earlier, in context of two other new ORFs that were located immediately downstream (closer to the centromere). As a result, both YLR154W-C and YLR154W-A needed to be changed.

YLR157W-A YLR157W-A YLR157W-D S000028677 Change Systematic Name 2005-03-28 YLR157W-A was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63. This name was incorrect because there was already an ORF named YLR157C-A, and new systematic names are assigned without regard to strandedness.

YLR157W-C YLR157W-B YLR157W-E S000028678 Change Systematic Name

Add MIPS Alias 2005-03-28 YLR157W-C was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63; this name is in conflict with another systematic name, YLR157C-C, which was described in Kessler MM, et al. (2003) Genome Res 13(2):264-71. These names are in conflict because new systematic names are assigned without regard to strandedness. Because MIPS and SGD had identical annotation for YLR157C-C, it was agreed to resolve this conflict by changing YLR157W-C/YLR157W-B to YLR157W-E.

Chromosome 14

YNL067W-A YNL067W-B YNL067W-A S000007623 Add MIPS Alias 2005-03-24 The systematic name YNL067W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YNL067W-A. YNL067W-A was published in Blandin G, et al. (2000) FEBS Lett 487(1):31-6.

YNL067W-B YNL067W-A YNL067W-B S000028810 Add MIPS Alias 2005-03-24 The systematic name YNL067W-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YNL067W-B. YNL067W-B was published in Oshiro G, et al. (2002) Genome Res 12(8):1210-20.

YNL097C-A YNL097C-B YNL097C-B S000028699 Change Systematic Name 2005-03-31 YNL097C-A was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63; this name is in conflict with another systematic name,YNL097W-A, also published in Kumar et al. These names are in conflict because new systematic names are assigned without regard to strandedness. It was agreed to resolve this conflict by changing YNL097C-A to YNL097C-B.

Chromosome 15

YOL013W-A YOL013W-B YOL013W-B S000007252 Change Systematic Name 2005-03-30 Neither YOL013W-A or YOL013W-B have ever been published. It appears that both were added based on data from Velculescu et al., (1997) Cell 88:243-251. However, MIPS and SGD assigned different names to these ORFs. It was agreed to use MIPS assignments.

YOL013W-B YOL013W-A YOL013W-A S000028811 Change Systematic Name 2005-03-30 Neither YOL013W-A or YOL013W-B have ever been published. It appears that both were added based on data from Velculescu et al., (1997) Cell 88:243-251. However, MIPS and SGD assigned different names to these ORFs. It was agreed to use the MIPS assignments.

Systematic name	SGDID	Change at SGD	Date of change	Comments
Previous SGD name	Previous MIPS name	Current
Chromosome 2
YBL039W-A	YBL039W-B	YBL039W-B	S000028517	Change Systematic Name	2005-03-30	"YBL039W-A" was published in Brachat S, et al. (2003) Genome Biol 4(7):R45. This name was incorrect because there was already an ORF named YBL039C-A, and new systematic names are assigned without regard to strandedness. YBL039C-A was published in Oshiro G, et al. (2002) Genome Res 12(8):1210-20.
YBL101W-B	TY2B_B	YBL100W-B	S000002149	Change Systematic Name; Add MIPS Alias	2005-03-29	"YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.
YBL101W-A	TY2A_B	YBL100W-A	S000002148	Change Systematic Name; Add MIPS Alias	2005-03-29	"YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.
YBL101W-C	YBL100W-C	YBL100W-C	S000028598	Change Systematic Name	2005-03-29	"YBL101W-C" was published in Kumar et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. This name was correct at the time at publication, as the centromere proximal ORF was YBL100W-B. However, YBL101W-A and YBL101W-B were incorrectly named, as the centromere proximal ORF is YBL100W, not YBL101C (YBL0101C is the telomere proximal flanking ORF). As a result, all three ORFs were changed from YBL101W-* to YBL100W-*.
Chromosome 3
YCL012C	YCL011C-A	YCL012C	S000029705	Add MIPS Alias	2005-03-24	The systematic name YCL011C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YCL012C. Although the name "YCL012C" was in conflict with a previously described but deleted ORF (YCL012W), it was agreed to keep the "YCL012C" name because it has been published in Zhang Z and Dietrich FS (2003) Yeast 20(8):731-8
Chromosome 4
YDL159W-A	YDL159W-B	YDL159W-A	S000007599	Add MIPS Alias	2005-03-24	The systematic name YDL159W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YDL159W-A. YDL159W-A" was published in Blandin G, et al. (2000) FEBS Lett 487(1):31-6.
YDL159C-B	YDL159C-A	YDL159C-B	S000028612	Add MIPS Alias	2005-03-24	The systematic name YDL159C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YDL159C-B. YDL159C-B was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63.
YDR524W-A	YDR524W-C	YDR524W-C	S000028740	Change Systematic Name	2005-03-28	"YDR524C-A" was published in Kumar et al. (2002). This name was incorrect because there was already an ORF named YDR524W-A, and new systematic names are assigned without regard to strandedness. However, the name YDR524W-A name has not been published, so it was agreed to keep the single published name and change YDR524W-A to YDR524W-C.
Chromosome 6
YFL031C-A	YFL030C-A	YFL031C-A	S000028629	Add MIPS Alias	2005-03-24	"YFL030C-A" was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63. This name was incorrect, because YFL030W is not the cetromere proximal ORF. The centromere proximal ORF is the overlapping ORF, YFL031W. The endpoint of YFL031W is closer to the centromere than is the endpoint of the new ORF, so the new ORF should be assigned the "YFL031" base name.
Chromosome 7
YGR169C-A	YGR169C-C	YGR169C-A	S000028521	Add MIPS Alias	2005-03-24	The systematic name YGR169C-C was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YGR169C-A. YGR169C-A was published in Brachat S, et al. (2003) Genome Biol 4(7):R45.
Chromosome 10
YJL127C-B	YJL127C-A	YJL127C-B	S000028522	Add MIPS Alias	2005-03-24	The systematic name YJL127C-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YJL127C-B. YJL127C-B was published in Brachat S, et al. (2003)Genome Biol 4(7):R45.
YJL127W-A	YJL127W-B	YJL127W-A	S000007612	Add MIPS Alias	2005-03-24	The systematic name YJL127W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YJL127W-A. YJL127W-A was published in Blandin G, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487(1):31-6.
YJL205C	YJL205C-A	YJL205C	S000003742	Add MIPS Alias	2003-04-02	YJL205C-A used to be the systematic name for this ORF. However, since this name was incorrectly named, this ORF name has been changed to YJL205C to properly represent the systematic ORF nomenclature. YJL205C-A is now an alias of YJL205C.
Chromosome 12
YLR154W-C	YLR154W-A	YLR154W-A	S000028675	Change Systematic Name	2005-04-01	Neither "YLR154W-A" or "YLR154W-C" have been published. Both ORFs were described in Kumar et al. (2002) Nat Biotechnol 20(1):58-63 and in Kessler MM, et al. (2003) Genome Res 13(2):264-71, but neither of these groups assigned systematic names. A careful characterization of the ORF at 452439-452624 was published in Coelho P, et al. (2002) Genes Dev 16(21):2755-60. However, these authors also did not assign a systematic name, but simply referred to the ORF by a gene name, TAR1. SGD added the ORF described by Coelho P, et al. without realizing that it had been described earlier, in context of two other new ORFs that were located immediately downstream (closer to the centromere). As a result, both YLR154W-C and YLR154W-A needed to be changed.
YLR154W-A	YLR154W-C	YLR154W-C	S000028422	Change Systematic Name	2005-04-01	Neither "YLR154W-A" or "YLR154W-C" have been published. Both ORFs were described in Kumar et al. (2002) Nat Biotechnol 20(1):58-63 and in Kessler MM, et al. (2003) Genome Res 13(2):264-71, but neither of these groups assigned systematic names. A careful characterization of the ORF at 452439-452624 was published in Coelho P, et al. (2002) Genes Dev 16(21):2755-60. However, these authors also did not assign a systematic name, but simply referred to the ORF by a gene name, TAR1. SGD added the ORF described by Coelho P, et al. without realizing that it had been described earlier, in context of two other new ORFs that were located immediately downstream (closer to the centromere). As a result, both YLR154W-C and YLR154W-A needed to be changed.
YLR157W-A	YLR157W-A	YLR157W-D	S000028677	Change Systematic Name	2005-03-28	YLR157W-A was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63. This name was incorrect because there was already an ORF named YLR157C-A, and new systematic names are assigned without regard to strandedness.
YLR157W-C	YLR157W-B	YLR157W-E	S000028678	Change Systematic Name Add MIPS Alias	2005-03-28	YLR157W-C was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63; this name is in conflict with another systematic name, YLR157C-C, which was described in Kessler MM, et al. (2003) Genome Res 13(2):264-71. These names are in conflict because new systematic names are assigned without regard to strandedness. Because MIPS and SGD had identical annotation for YLR157C-C, it was agreed to resolve this conflict by changing YLR157W-C/YLR157W-B to YLR157W-E.
Chromosome 14
YNL067W-A	YNL067W-B	YNL067W-A	S000007623	Add MIPS Alias	2005-03-24	The systematic name YNL067W-B was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YNL067W-A. YNL067W-A was published in Blandin G, et al. (2000) FEBS Lett 487(1):31-6.
YNL067W-B	YNL067W-A	YNL067W-B	S000028810	Add MIPS Alias	2005-03-24	The systematic name YNL067W-A was temporarily used for this ORF at MIPS. This name was never published, and MIPS has corrected the systematic name to YNL067W-B. YNL067W-B was published in Oshiro G, et al. (2002) Genome Res 12(8):1210-20.
YNL097C-A	YNL097C-B	YNL097C-B	S000028699	Change Systematic Name	2005-03-31	YNL097C-A was published in Kumar et al. (2002) Nat Biotechnol 20(1):58-63; this name is in conflict with another systematic name,YNL097W-A, also published in Kumar et al. These names are in conflict because new systematic names are assigned without regard to strandedness. It was agreed to resolve this conflict by changing YNL097C-A to YNL097C-B.
Chromosome 15
YOL013W-A	YOL013W-B	YOL013W-B	S000007252	Change Systematic Name	2005-03-30	Neither YOL013W-A or YOL013W-B have ever been published. It appears that both were added based on data from Velculescu et al., (1997) Cell 88:243-251. However, MIPS and SGD assigned different names to these ORFs. It was agreed to use MIPS assignments.
YOL013W-B	YOL013W-A	YOL013W-A	S000028811	Change Systematic Name	2005-03-30	Neither YOL013W-A or YOL013W-B have ever been published. It appears that both were added based on data from Velculescu et al., (1997) Cell 88:243-251. However, MIPS and SGD assigned different names to these ORFs. It was agreed to use the MIPS assignments.

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