Difference between revisions of "Chromosome V History"

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(Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome V systematic reference sequence since its intial release on 1996-07-31. <br> *The seq...")
 
(Annotation Changes without sequence changes)
 
(6 intermediate revisions by the same user not shown)
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| Substitution
 
| Substitution
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| A
 
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| || colspan="6" | A single nucleotide substitution within the coding region of RAD4/YER162C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 223 is now Valine rather than Glutamic Acid.
 
| || colspan="6" | A single nucleotide substitution within the coding region of RAD4/YER162C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 223 is now Valine rather than Glutamic Acid.
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'''Wang X, et al.''' (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85. <br>
 
'''Wang X, et al.''' (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85. <br>
 
[https://www.yeastgenome.org/reference/S000051920 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8816449 PubMed] | [https://mcb.asm.org/content/16/10/5375 Full-Text] <br>
 
[https://www.yeastgenome.org/reference/S000051920 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8816449 PubMed] | [https://mcb.asm.org/content/16/10/5375 Full-Text] <br>
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 +
|}
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<br><br>
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=Annotation Changes ''without sequence changes''=
 +
{| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
 +
! Date  !! Affected Features
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS507 ARS507], [https://www.yeastgenome.org/locus/ARS508 ARS508], [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS512 ARS512], [https://www.yeastgenome.org/locus/ARS513.7 ARS513.7], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS516 ARS516], [https://www.yeastgenome.org/locus/ARS518 ARS518], [https://www.yeastgenome.org/locus/ARS520 ARS520], [https://www.yeastgenome.org/locus/ARS523 ARS523] <br>
 +
As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome V based on Liachko et al. 2013: ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS503 ARS503], [https://www.yeastgenome.org/locus/ARS507 ARS507], [https://www.yeastgenome.org/locus/ARS510 ARS510],  [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS516 ARS516],  [https://www.yeastgenome.org/locus/ARS520 ARS520], [https://www.yeastgenome.org/locus/ARS523 ARS523] <br>
 +
The chromosomal coordinates of the following ARS elements on Chromosome V were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS513.5 ARS513.5], [https://www.yeastgenome.org/locus/ARS513.7 ARS513.7] <br>
 +
The following new ARS elements on Chromosome V were added to the genome annotation based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS513.5, ARS513.7. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-18
 +
| [https://www.yeastgenome.org/locus/YER109C YER109C] <br>
 +
The feature_type annotation of FLO8/YER109C was changed from ORF to blocked_reading_frame (SO:0000718) as part of SGD's genome annotation revision R64.2. <br> <br>
 +
|-
 +
| 2014-07-18
 +
| [https://www.yeastgenome.org/locus/YER038W-A YER038W-A] <br>
 +
ORF YER038W-A was upgraded from 'Dubious' to 'Uncharacterized' on 2014-01-30 because its protein product was found in the mitochondria in both the Sickmann et al 2003 and Reinders et al 2006 studies. <br> <br>
 +
'''Sickmann A, et al.''' (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12. <br>
 +
[https://www.yeastgenome.org/reference/S000075100 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/14576278 PubMed] | [https://www.pnas.org/content/100/23/13207 Full-Text] | [https://www.pnas.org/content/suppl/2003/10/17/2135385100.DC1 Web Supplement] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=14576278&db=pmid YFGdb] <br>
 +
'''Reinders J, et al.''' (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54. <br>
 +
[https://www.yeastgenome.org/reference/S000117178 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/16823961 PubMed] | [https://pubs.acs.org/doi/abs/10.1021/pr050477f Full-Text] |  [https://pubs.acs.org/doi/abs/10.1021/pr050477f Web Supplement] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=16823961&db=pmid YFGdb] <br>
 +
|-
 +
| 2007-07-09
 +
| [https://www.yeastgenome.org/locus/YEL003W YEL003W] <br>
 +
The start of GIM4/YEL003W was moved 52 nt upstream, and an intron was added at relative coordinates 20-107, based on GenBank EF123144, Juneau et al. 2007, and Miura et al. 2006. According to Juneau et al. 2007, the intron is "inefficiently spliced" (splicing rate = 72%). ''The old coding coordinates were 148227..148598 (372 nt, 123 aa), and the new coding coordinates are 148175..148193,148282..148598 (1..19,108..424; 111 aa).''<br> <br>
 +
'''Miura F, et al.''' (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. <br>
 +
[https://www.yeastgenome.org/reference/S000119659 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/17101987 PubMed] | [https://www.pnas.org/content/103/47/17846.long Full-Text] <br>
 +
'''Juneau K, et al.''' (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.
 +
<br>
 +
|-
 +
| 2007-04-04
 +
| [https://www.yeastgenome.org/locus/YER131W YER131W] <br>
 +
RPS26B/YER131W mRNA contains an intron in the 5' untranslated region (UTR).<br> <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
'''Miura F, et al.''' (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. <br>
 +
[https://www.yeastgenome.org/reference/S000119659 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/17101987 PubMed] | [https://www.pnas.org/content/103/47/17846.long Full-Text] <br>
 +
'''Juneau K, et al.''' (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.
 +
<br>
 +
|-
 +
| 2007-04-04
 +
| [https://www.yeastgenome.org/locus/YER102W YER102W] <br>
 +
RPS8B/YER102W mRNA contains an intron in the 5' untranslated region (UTR).<br> <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
'''Miura F, et al.''' (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. <br>
 +
[https://www.yeastgenome.org/reference/S000119659 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/17101987 PubMed] | [https://www.pnas.org/content/103/47/17846.long Full-Text] <br>
 +
'''Juneau K, et al.''' (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.
 +
<br>
 +
|-
 +
| 2007-04-03
 +
| [https://www.yeastgenome.org/locus/YERCdelta8 YERCdelta8] <br>
 +
YERCdelta8, a Ty1 LTR on Chromosome V, was mistakenly annotated on the wrong strand (i.e., on Watson instead of Crick). The error has now been corrected.<br> <br>
 +
|-
 +
| 2006-10-02
 +
| [https://www.yeastgenome.org/locus/ARS516 ARS516] <br>
 +
The coordinates of ARS516 were updated based on Nieduszynski et al. 2006.<br> <br>
 +
'''Nieduszynski CA, et al.''' (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. <br>
 +
[https://www.yeastgenome.org/reference/S000117321 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/16847347 PubMed] | [http://genesdev.cshlp.org/content/20/14/1874.long Full-Text] | [http://genesdev.cshlp.org/content/20/14/1874/suppl/DC1 Web Supplement]<br>
 +
|-
 +
| 2006-09-07
 +
| [https://www.yeastgenome.org/locus/ARS507 ARS507], [https://www.yeastgenome.org/locus/ARS508 ARS508], [https://www.yeastgenome.org/locus/ARS510 ARS510], [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS512 ARS512], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS517 ARS517], [https://www.yeastgenome.org/locus/ARS518 ARS518], [https://www.yeastgenome.org/locus/ARS522 ARS522] <br>
 +
The coordinates of the following ARS elements on Chromosome V were updated based on Nieduszynski et al. 2006: ARS507, ARS508, ARS510, ARS511, ARS512, ARS514, ARS517, ARS518, ARS522/501. <br> <br>
 +
'''Nieduszynski CA, et al.''' (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. <br>
 +
[https://www.yeastgenome.org/reference/S000117321 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/16847347 PubMed] | [http://genesdev.cshlp.org/content/20/14/1874.long Full-Text] | [http://genesdev.cshlp.org/content/20/14/1874/suppl/DC1 Web Supplement]<br>
 +
|-
 +
| 2006-05-09
 +
| [https://www.yeastgenome.org/locus/YEL038W YEL038W] <br>
 +
The proposal by Kellis et al. was re-examined in light of sequence data from S. kudriavzevii (another sensu stricto strain published by Cliften et al.). The S. kudriavzevii sequence supported the start codon suggested by Kellis et al., so the start site for UTR4/YEL038W be moved 42 nt (14 codons) downstream. <br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2006-05-08
 +
| [https://www.yeastgenome.org/locus/CEN5 CEN5] <br>
 +
The previously annotated boundaries of CEN5 were adjusted to coincide with the 5' end of CDEI and the 3' end of CDEIII, to more accurately reflect current knowledge regarding centromere structure in ''Saccharomyces cerevisiae''. <br> <br>
 +
'''Wieland G, et al.''' (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60. <br>
 +
[https://www.yeastgenome.org/reference/S000059647 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11222754 PubMed] | [https://academic.oup.com/nar/article/29/5/1054/2381189 Full-Text]<br>
 +
'''Espelin CW, et al.''' (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68. <br>
 +
[https://www.yeastgenome.org/reference/S000074756 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/13679521 PubMed] | [https://www.molbiolcell.org/doi/full/10.1091/mbc.e02-08-0533?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed Full-Text]<br>
 +
|-
 +
| 2005-11-29
 +
| [https://www.yeastgenome.org/locus/snR80 snR80] <br>
 +
New snoRNA added to genome annotation. <br> <br>
 +
'''Schattner P, et al.''' (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 32(14):4281-96. <br>
 +
[https://www.yeastgenome.org/reference/S000081218 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/15306656 PubMed] | [https://academic.oup.com/nar/article/32/14/4281/1279684/ Full-Text] <br>
 +
|-
 +
| 2005-11-29
 +
| [https://www.yeastgenome.org/locus/YER030W YER030W] <br>
 +
The start site of YER030W is being moved 21 bp downstream from 213415 to 213436 because the 5' SAGE data used by Zhang & Dietrich 2005 to study transcription start sites confirmed the initial suggestion by Kellis et al. 2003 that this change be made. The size of the predicted protein is reduced from 160 aa to 153 aa.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Zhang Z and Dietrich FS''' (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51. <br>
 +
[https://www.yeastgenome.org/reference/S000082006 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/15905473 PubMed] | [https://academic.oup.com/nar/article/33/9/2838/2401448 Full-Text] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=15905473&db=pmid YFGdb]<br>
 +
|-
 +
| 2005-11-28
 +
| [https://www.yeastgenome.org/locus/YER050C YER050C] <br>
 +
The start site of RSM18/YER050C is being moved 192 bp downstream from 254578 to 254386, based on 5' SAGE data used by Zhang & Dietrich 2005 to study transcription start sites.<br> <br>
 +
'''Zhang Z and Dietrich FS''' (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51. <br>
 +
[https://www.yeastgenome.org/reference/S000082006 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/15905473 PubMed] | [https://academic.oup.com/nar/article/33/9/2838/2401448 Full-Text] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=15905473&db=pmid YFGdb]<br>
 +
|-
 +
| 2004-10-19
 +
| [https://www.yeastgenome.org/locus/ARS502 ARS502], [https://www.yeastgenome.org/locus/ARS503 ARS503], [https://www.yeastgenome.org/locus/ARS504 ARS504], [https://www.yeastgenome.org/locus/ARS507 ARS50], [https://www.yeastgenome.org/locus/ARS508 ARS508], [https://www.yeastgenome.org/locus/ARS510 ARS510], [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS512 ARS512], [https://www.yeastgenome.org/locus/ARS513 ARS513], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS515 ARS515], [https://www.yeastgenome.org/locus/ARS516 ARS516], [https://www.yeastgenome.org/locus/ARS517 ARS517], [https://www.yeastgenome.org/locus/ARS518 ARS518], [https://www.yeastgenome.org/locus/ARS519 ARS519], [https://www.yeastgenome.org/locus/ARS520 ARS520], [https://www.yeastgenome.org/locus/ARS521 ARS521], [https://www.yeastgenome.org/locus/ARS522 ARS522], [https://www.yeastgenome.org/locus/ARS523 ARS523] <br>
 +
The following ARS elements on Chromosome V were added to SGD based on Tanaka et al. 1996 and Raghuraman et al. 2001: ARS502, ARS503, ARS504, ARS507, ARS508, ARS510, ARS511, ARS512, ARS513, ARS514, ARS515, ARS516, ARS517, ARS518, ARS519, ARS520, ARS521, ARS522, ARS523. <br> <br>
 +
'''Tanaka S, et al.''' (1996) Systematic mapping of autonomously replicating sequences on chromosome V of Saccharomyces cerevisiae using a novel strategy. Yeast 12(2):101-13. <br>
 +
[https://www.yeastgenome.org/reference/S000046131 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8686374 PubMed] | [https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0061%28199602%2912%3A2%3C101%3A%3AAID-YEA885%3E3.0.CO%3B2-2 Full-Text] <br>
 +
'''Raghuraman MK, et al.''' (2001) Replication dynamics of the yeast genome. Science 294(5540):115-21. <br>
 +
[https://www.yeastgenome.org/reference/S000113866 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11588253 PubMed] | [https://science.sciencemag.org/content/294/5540/115.long Full-Text] <br>
 +
|-
 +
| 2004-10-12
 +
| [https://www.yeastgenome.org/locus/CEN5 CEN5] <br>
 +
Centromeric DNA elements CDEI, CDEII, and CDEIII were annotated based on Wieland et al. 2001 and Espelin et al. 2003. <br> <br>
 +
'''Wieland G, et al.''' (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60. <br>
 +
[https://www.yeastgenome.org/reference/S000059647 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11222754 PubMed] | [https://academic.oup.com/nar/article/29/5/1054/2381189 Full-Text]<br>
 +
'''Espelin CW, et al.''' (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68. <br>
 +
[https://www.yeastgenome.org/reference/S000074756 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/13679521 PubMed] | [https://www.molbiolcell.org/doi/full/10.1091/mbc.e02-08-0533?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed Full-Text]<br>
 +
|-
 +
| 2004-10-08
 +
| [https://www.yeastgenome.org/locus/SCR1 SCR1] <br>
 +
The coordinates of the small cytoplasmic RNA SCR1 were corrected to match the sequence determined by Felici, et al. and reported in the GenBank entry M28116. <br> <br>
 +
'''Felici F, et al.''' (1989) The most abundant small cytoplasmic RNA of Saccharomyces cerevisiae has an important function required for normal cell growth. Mol Cell Biol 9(8):3260-8. <br>
 +
[https://www.yeastgenome.org/reference/S000055283 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/2477683 PubMed] | [https://mcb.asm.org/content/9/8/3260.long Full-Text] <br>
 +
|-
 +
| 2004-08-27
 +
| [https://www.yeastgenome.org/locus/YER090C-A YER090C-A] <br>
 +
The ORF YER090C-A was added per Oshiro et al. 2002. <br> <br>
 +
'''Oshiro G, et al.''' (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20. <br>
 +
[https://www.yeastgenome.org/reference/S000073672 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12176929 PubMed] | [https://genome.cshlp.org/content/12/8/1210.long Full-Text] | [https://genome.cshlp.org/content/12/8/1210/suppl/DC1 Web Supplement] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=12176929&db=pmid YFGdb] <br>
 +
|-
 +
| 2004-04-01
 +
| [https://www.yeastgenome.org/locus/RUF4 RUF4] <br>
 +
Feature annotation removed per John McCutcheon and Sean Eddy. <br> <br>
 +
'''McCutcheon JP and Eddy SR''' (2004) Detailed correction to: Computational identification of noncoding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res. 31:4119-4128, 2003. <br>
 +
[https://www.yeastgenome.org/reference/S000074006 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12853629 PubMed] | [https://academic.oup.com/nar/article/31/14/4119/2904330#55548715 Full-Text] <br>
 +
|-
 +
| 2004-01-08
 +
| [https://www.yeastgenome.org/locus/YER074W-A YER074W-A] <br>
 +
Both introns in YER074W-A were extended 1 bp in the 5' direction and 2 bp in the 3' direction based on conserved splice site sequences in other fungal species as predicted by Blandin et al. 2000.<br> <br>
 +
'''Blandin G, et al.''' (2000) Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487(1):31-6. <br>
 +
[https://www.yeastgenome.org/reference/S000065690 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11152879 PubMed] | [https://febs.onlinelibrary.wiley.com/doi/full/10.1016/S0014-5793%2800%2902275-4 Full-Text]<br>
 +
|-
 +
| 2003-10-29
 +
| [https://www.yeastgenome.org/locus/SRG1 SRG1] <br>
 +
This non-coding RNA feature was annotated based on information from Fred Winston; the SRG1 TATA begins at position 322124, the transcription start sites are at positions 322208 and 322209, and the size of the transcript is approximately 550 bases as determined by Northern analysis.<br> <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/YER178W YER178W] <br>
 +
Based on the automated comparison of closely-related ''Saccharomyces'' species by Kellis et al., the start site for PDA1/YER178W was moved 69 nt (23 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of ''Saccharomyces'' species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine; 3) The predicted protein translated from the conserved methionine contains a predicted mitochondrial targeting signal sequence (using both MitoProt and Predotar), while the predicted protein translated from the currently annotated ''S. cerevisiae'' start codon does not.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/YER032W YER032W] <br>
 +
Based on the automated comparison of closely-related ''Saccharomyces'' species by Kellis et al., the start site for FIR1/YER032W was moved 147 nt (49 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of ''Saccharomyces'' species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/YER083C YER083C] <br>
 +
Based on the automated comparison of closely-related ''Saccharomyces'' species by Kellis et al., the start site for YER083C was moved 66 nt (22 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of ''Saccharomyces'' species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/YEL062W YEL062W] <br>
 +
Based on the automated comparison of closely-related ''Saccharomyces'' species by Kellis et al., the start site for NPR2/YEL062W was moved 27 nt (9 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of ''Saccharomyces'' species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/YEL061C YEL061C] <br>
 +
Based on the automated comparison of closely-related ''Saccharomyces'' species by Kellis et al., the start site for CIN8/YEL061C was moved 114 nt (38 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of ''Saccharomyces'' species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.<br> <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata] <br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
|-
 +
| 2003-09-22
 +
| [https://www.yeastgenome.org/locus/TEL05L TEL05L], [https://www.yeastgenome.org/locus/TEL05R TEL05R] <br>
 +
The chromosomal locations for the following telomeric elements on Chromosome V were generously provided by Ed Louis and Dave Barton (University of Leicester, UK): TEL05L, TEL05L-XC, TEL05L-YP, TEL05R, TEL05R-XC, TEL05R-XR, TEL05R-YP. <br><br>
 +
Note that both TEL05L and TEL05R have telomeric repeats (TEL05L-TR and TEL05R-TR), but they are missing from the genome annotation due to sequencing difficulties encountered during the initial genome sequencing efforts in the 1990s. <br>
 +
|-
 +
| 2003-07-29
 +
| [https://www.yeastgenome.org/locus/YEL009C-A YEL009C-A], [https://www.yeastgenome.org/locus/YEL018C-A YEL018C-A], [https://www.yeastgenome.org/locus/YEL034C-A YEL034C-A], [https://www.yeastgenome.org/locus/YEL053W-A YEL053W-A], [https://www.yeastgenome.org/locus/YER006C-A YER006C-A], [https://www.yeastgenome.org/locus/YER038W-A YER038W-A], [https://www.yeastgenome.org/locus/YER046W-A YER046W-A], [https://www.yeastgenome.org/locus/YER067C-A YER067C-A], [https://www.yeastgenome.org/locus/YER068C-A YER068C-A], [https://www.yeastgenome.org/locus/YER076W-A YER076W-A], [https://www.yeastgenome.org/locus/YER079C-A YER079C-A], [https://www.yeastgenome.org/locus/YER084W-A YER084W-A], [https://www.yeastgenome.org/locus/YER087C-A YER087C-A], [https://www.yeastgenome.org/locus/YER088C-A YER088C-A], [https://www.yeastgenome.org/locus/YER107W-A YER107W-A], [https://www.yeastgenome.org/locus/YER133W-A YER133W-A], [https://www.yeastgenome.org/locus/YER137W-A YER137W-A], [https://www.yeastgenome.org/locus/YER145C-A YER145C-A], [https://www.yeastgenome.org/locus/YER147C-A YER147C-A], [https://www.yeastgenome.org/locus/YER148W-A YER148W-A], [https://www.yeastgenome.org/locus/YER152W-A YER152W-A], [https://www.yeastgenome.org/locus/YER165C-A YER165C-A], [https://www.yeastgenome.org/locus/YER172C-A YER172C-A], [https://www.yeastgenome.org/locus/YER188C-A YER188C-A] <br>
 +
The coordinates for the following ORFs on Chromosome V were provided by [https://bioinformatik.wzw.tum.de/index.php?id=63 MIPS]: YEL009C-A, YEL018C-A, YEL034C-A, YEL053W-A, YER006C-A, YER038W-A, YER046W-A, YER067C-A, YER068C-A, YER076W-A, YER079C-A, YER084W-A, YER087C-A, YER088C-A, YER107W-A, YER133W-A, YER137W-A, YER145C-A, YER147C-A, YER148W-A, YER152W-A, YER165C-A, YER172C-A, YER188C-A.<br><br>
 +
|-
 +
| 2003-07-29
 +
| [https://www.yeastgenome.org/locus/YEL008C-A YEL008C-A], [https://www.yeastgenome.org/locus/YEL030C-A YEL030C-A], [https://www.yeastgenome.org/locus/YEL032C-A YEL032C-A], [https://www.yeastgenome.org/locus/YEL077W-A YEL077W-A], [https://www.yeastgenome.org/locus/YER023C-A YER023C-A], [https://www.yeastgenome.org/locus/YER088W-B YER088W-B], [https://www.yeastgenome.org/locus/YER158W-A YER158W-A], [https://www.yeastgenome.org/locus/YER175W-A YER175W-A], [https://www.yeastgenome.org/locus/YER190C-A YER190C-A], [https://www.yeastgenome.org/locus/YER190C-B YER190C-B] <br>
 +
The coordinates for the following ORFs on Chromosome V were provided by Kumar et al. 2002: YEL008C-A, YEL030C-A, YEL032C-A, YEL077W-A, YER023C-A, YER088W-B, YER158W-A, YER175W-A, YER190C-A, YER190C-B. <br><br>
 +
'''Kumar A, et al.''' (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. <br>
 +
[https://www.yeastgenome.org/reference/S000073673 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11753363 PubMed] | [https://www.nature.com/articles/nbt0102-58 Full-Text] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=11753363&db=pmid YFGdb] | [https://www.yeastgenome.org/reference/S000141796 Comments & Errata] <br>
 +
|-
 +
| 2003-07-29
 +
| [https://www.yeastgenome.org/locus/YEL020C-B YEL020C-B], [https://www.yeastgenome.org/locus/YEL050W-A YEL050W-A], [https://www.yeastgenome.org/locus/YER078W-A YER078W-A] <br>
 +
The coordinates for the following ORFs on Chromosome V were provided by Kessler et al. 2003: YEL020C-B, YEL050W-A, YER078W-A. <br><br>
 +
'''Kessler MM, et al.''' (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71. <br>
 +
[https://www.yeastgenome.org/reference/S000073671 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12566404 PubMed] | [https://genome.cshlp.org/content/13/2/264.long Full-Text] <br>
 +
|-
 +
| 2003-03-07
 +
| [https://www.yeastgenome.org/locus/YER180C-A YER180C-A] <br>
 +
ORF YER180C-A was added to SGD based on Panic et al. 2003. <br><br>
 +
'''Panic B, et al.''' (2003) The ARF-like GTPases Arl1p and Arl3p act in a pathway that interacts with vesicle-tethering factors at the Golgi apparatus. Curr Biol 13(5):405-10. <br>
 +
[https://www.yeastgenome.org/reference/S000072666 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12620189 PubMed] | [https://www.sciencedirect.com/science/article/pii/S0960982203000915?via%3Dihub Full-Text] | [https://www.ncbi.nlm.nih.gov/pubmed/12620205 Comments & Errata] <br>
 +
|-
 +
| 2003-03-06
 +
| [https://www.yeastgenome.org/locus/RUF4 RUF4] <br>
 +
Thanks to John McCutcheon and Sean Eddy for providing the coordinates for the following RNA features: SNR82, SNR83, SNR84, RUF4, RUF5-1, RUF5-2, RUF6, RUF7, and RUF8. <br><br>
 +
'''McCutcheon JP and Eddy SR''' (2003) Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 31(14):4119-28. <br>
 +
[https://www.yeastgenome.org/reference/S000074006 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12853629 PubMed] | [https://academic.oup.com/nar/article/31/14/4119/2904330 Full-Text] <br>
 +
|-
 +
| 2002-11-19
 +
| [https://www.yeastgenome.org/locus/YERCTy1-1 YERCTy1-1], [https://www.yeastgenome.org/locus/YERWdelta18 YERWdelta18] <br>
 +
The YERWdelta18 element was initially mistakenly annotated as a separate LTR, though its coordinates completely overlapped with the full length transposon https://www.yeastgenome.org/locus/YERCTy1-1 YERCTy1-1]. Thus, YERWdelta18 has been deleted from the database. <br><br>
 +
|-
 +
| 2002-11-19
 +
| [https://www.yeastgenome.org/locus/YERCTy1-2 YERCTy1-2], [https://www.yeastgenome.org/locus/YERCsigma4 YERCsigma4] <br>
 +
The YERCsigma4 element was initially mistakenly annotated as a separate sigma LTR, though its coordinates completely overlapped with the full length transposon [https://www.yeastgenome.org/locus/YERCTy1-2 YERCTy1-2], which contains delta elements, not sigma elements. Thus, YERCsigma4 has been deleted from the genome annotation. <br><br>
 +
|-
 +
| 2000-12-01
 +
| [https://www.yeastgenome.org/locus/YER056C-A YER056C-A] <br>
 +
The intron of YER056C-A was moved 2 nucleotides upstream. The genomic sequence remains unchanged, but the coding sequence is now only very slightly altered. R''elative coordinates change from 1-39..437-763 to 1-37..435-780, and chromosomal coordinates change from 270183-270145..269747-269421 to 270183-270147..269749-269421.'' <br><br>
 +
|-
 +
| 2000-12-01
 +
| [https://www.yeastgenome.org/locus/YEL012W YEL012W] <br>
 +
The start site of YEL012W was moved 159 nucleotides upstream, and an intron was added at relative coordinates 6-128. The stop remains unchanged. ''Relative coordinates change from 1-621 to 1-5..129-780, and chromosomal coordinates change from 131931-132551 to 131772-131776..131900-132551.'' <br><br>
 +
|-
 +
| 1999-07-17
 +
| [https://www.yeastgenome.org/locus/YER060W-A YER060W-A] <br>
 +
YER060W-A/FCY22 was originally incorrectly annotated as being identical to its neighboring ORF YER060W/FCY21, at coordinates 274565-276151 (1587 nucleotides long). This error has been corrected, and the coordinates of YER060W-A/FCY22 are now 276570-278162 (1593 nt). Sequence files have been updated accordingly. <br><br>
 +
|-
 +
| 1999-07-17
 +
| [https://www.yeastgenome.org/locus/YER108C YER108C], [https://www.yeastgenome.org/locus/YER109C YER109C] <br>
 +
YER108C and YER109C were originally annotated as two separate open reading frames, but it has been demonstrated that they correspond to the FLO8 gene, which contains a nonsense mutation in the reference strain S288C - an A to G transition at position 431, changing amino acid 144 from a Trp to a stop. Therefore, they have been fused into one reading frame with an internal stop codon. <br><br>
 +
'''Liu H, et al.''' (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144(3):967-78. <br>
 +
[https://www.yeastgenome.org/reference/S000054124 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8913742 PubMed] | [https://www.genetics.org/content/144/3/967.long Full-Text] <br>
 +
|-
 +
| 1998-05-21
 +
| [https://www.yeastgenome.org/locus/YER048W-A YER048W-A], [https://www.yeastgenome.org/locus/YER091C-A YER091C-A], [https://www.yeastgenome.org/locus/YER138W-A YER138W-A] <br>
 +
The following 27 ORFs were added to the genome annotation based on Velculescu et al. 1997: YBL091C-A, YBL107W-A, YCR018C-A, YCR102W-A, YDL130W-A, YDR034C-A, YDR034W-B, YDR363W-A, YDR525W-A, YER048W-A, YER091C-A, YER138W-A, YGR122C-A, YIR020W-B, YKL033W-A, YKL053C-A, YKL162C-A, YLL018C-A, YLR262C-A, YML081C-A, YMR046W-A, YMR158C-B, YMR194C-A, YNR032C-A, YOL013W-A, YOR298C-A, and YPR002C-A. <br><br>
 +
The coordinates of the tag sequences along the genome were determined and each tag was classified into one of these four categories: 1) class 1 - within an existing ORF, 2) class 2 - within 500 bp downstream of existing an ORF, 3) class 4 - opposite of an existing ORF, or 4) class 3 - none of the above. The regions between two existing ORFs which contained one or more unique class 3 tags (number 4) above) were examined for potential coding sequences in which the unique tag was located either within the coding sequence or 500bp downstream of this sequence. BLASTP analysis was then performed for each potential ORF meeting these criteria against the non-redundant (nr) NCBI dataset, and those with a P value exponent of -6 or less were analyzed further. The BLAST results were analyzed on an individual basis for each potential ORF meeting the above criteria. Those potential ORFs which exhibited reasonable homology to other proteins, and did not appear to be matched with other proteins based on homology to repetitive sequences alone, were identified and entered into SGD. <br><br>
 +
'''Velculescu VE, et al.''' (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51. <br>
 +
[https://www.yeastgenome.org/reference/S000058021 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/9008165 PubMed] | [https://www.sciencedirect.com/science/article/pii/S0092867400818450?via%3Dihub Full-Text] | [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=9008165&db=pmid YFGdb] <br>
 +
 +
|}

Latest revision as of 12:50, 4 October 2019

This page lists all sequence and annotation changes that have been made to the Chromosome V systematic reference sequence since its intial release on 1996-07-31.

  • The sequence of Chromosome V has been updated 20 times, affecting 19 features.
  • The annotation of Chromosome V has been updated 41 times, affecting 92 features.
  • Current and past versions can be obtained from SGD's Download site.


Sequence Changes

Date Affected Features Start Coordinate of Change End Coordinate of Change Type of Change Old Sequence New Sequence
2011-02-03 YER075C 308627 308627 Substitution C G
308984 308984 Substitution G T
309047 309047 Substitution G C
Nucleotide substitutions within the coding region of PTP3/YER075C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 717 is now Alanine rather than Proline, and residue 738 is now Lysine rather than Q, and residue 857 is now Glutamine rather than Glutamic Acid.
New   308581  GTCATAAATGAAAATAAATTGATTAATGTTCTGGACCATGGATATTCGTTGCTTTCTAAA  308640
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Old   308577  GTCATAAATGAAAATAAATTGATTAATGTTCTGGACCATGGATATTCGTTCCTTTCTAAA  308636

New   308941  TAACAATTCATAAGGTTTCTCTTGATCATGATATGTTAGCAGAATTTTTCTTATGAGAAT  309000
              ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old   308937  TAACAATTCATAAGGTTTCTCTTGATCATGATATGTTAGCAGAATTTGTCTTATGAGAAT  308996
New   309001  TGCGTCATCATCATCATCATCATCATCATCACAAGCAGCAGCAGTAACAGCAATATTACT  309060
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Old   308997  TGCGTCATCATCATCATCATCATCATCATCACAAGCAGCAGCAGTAACAGGAATATTACT  309056

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER162C 502222 502222 Substitution T A
A single nucleotide substitution within the coding region of RAD4/YER162C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 223 is now Valine rather than Glutamic Acid.
New   502201  CTTTCCAGGTTCTCATATAAAGTCCCACATTATCATATTTTTTAGTGATCTTCCAGTGTT  502260
              |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Old   502196  CTTTCCAGGTTCTCATATAAAGTCCCTCATTATCATATTTTTTAGTGATCTTCCAGTGTT  502255

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER041W 232634 232634 Substitution C G
A single nucleotide substitution within the coding region of YEN1/YER041W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 59 is now Alanine rather than Proline.
New   232621  ATATAGATATAAGCGCCAGATCTAGATCAAGATCAAGGAGTCCTACCCGTTCTCCGCGTG  232680
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old   232620  ATATAGATATAAGCCCCAGATCTAGATCAAGATCAAGGAGTCCTACCCGTTCTCCGCGTG  232679

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER061C 278525 278526 Substitution CG GC
Nucleotide changes within the coding region of CEM1/YER061C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 367 is now Alanine rather than Arginine.
New   278521  GCGCCAGCTGCACCTAAAAGATGGCCAATTGCACCTTTGTTACTGGATATGTACAGTGGC  278580
              ||||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||
Old   278519  GCGCCACGTGCACCTAAAAGATGGCCAATTGCACCTTTGTTACTGGATATGTACAGTGGC  278578

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER073W 305258 305258 Substitution G A
A single nucleotide substitution within the coding region of ALD5/YER073W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 411 is now Glutamic Acid rather than Glycine.
New   305221  GGTTATTTTGTCAAGCCAACAGTGTTTGCTGATGTCAAAGAAGATATGAGAATTGTTAAG  305280
              |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Old   305218  GGTTATTTTGTCAAGCCAACAGTGTTTGCTGATGTCAAAGGAGATATGAGAATTGTTAAG  305277

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YEL007W, YEL008W 141112 141112 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs YEL008W and YEL007W.
 New    141061  GCAATGATCTGTCCAACTCACCGAAACAAGAAAAAATTTTGCGTTTTTTTTTTCCTACAAATCCCCCATT  141130
               |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Old    141061  GCAATGATCTGTCCAACTCACCGAAACAAGAAAAAATTTTGCGTTTTTTTTT-CCTACAAATCCCCCATT  141129

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YEL070W, YEL071W 18079 18079 Substitution A T
A single nucleotide substitution was made in the intergenic region between ORFs DLD3/YEL071W and DSF1/YEL070W.
New    18061   ATCTCCTGATTGCGTACTTCAAAAAGTGTTCGTCCATTTTTTCTTTACTACATTAGATAA  18120
               |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Old    18061   ATCTCCTGATTGCGTACTACAAAAAGTGTTCGTCCATTTTTTCTTTACTACATTAGATAA  18120

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER056C, YER056C-A 268857 268857 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs FCY2/YER056C and RPL34A/YER056C-A.
New    268801  AACTTGGTTGAAAGTGGCTGAATTTACGACGTAATCTGTCTTGACATCTTTTTTTTTTTCAGCGAGCATT  268870
               |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Old    268800  AACTTGGTTGAAAGTGGCTGAATTTACGACGTAATCTGTCTTGACATCTTTTTTTTTT-CAGCGAGCATT  268868

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER072W, YER073W 303532 303532 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs VTC1/YER072W and ALD5/YER073W.
New    303481  CCGTTTACACATCAATGATAAATAAGTATACAAAAAGGGTTCCATTTTTTTTTTTGGCCGCTACCGGACT  303550
               |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old    303479  CCGTTTACACATCAATGATAAATAAGTATACAAAAAGGGTTCCATTTTTTTTTT-GGCCGCTACCGGACT  303547

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER133W, tH(GUG)E2 434284 434284 Substitution C T
A single nucleotide substitution was made in the intergenic region between GLC7/YER133W and tH(GUG)E2.
New    434281  CAATTTTTCTTTATTTTCTTTTATTACTATTATCATTACTATTATTATTAGTATTATTAT  434340
               ||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    434277  CAATTTTCCTTTATTTTCTTTTATTACTATTATCATTACTATTATTATTAGTATTATTAT  434336

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER138W-A, YER139C 449959 449959 Insertion A
A single nucleotide insertion was made in the intergenic region between ORFs YER138W-A and RTR1/YER139C.
New    449941  GTGGGTTTCCTATGTTCTCGAAGAGAGCTTCAAGTGTATTCTATAAACTAAGAATATTAG  450000
               ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Old    449937  GTGGGTTTCCTATGTTCTCGAAG-GAGCTTCAAGTGTATTCTATAAACTAAGAATATTAG  449995

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 YER073W, ER074W 305968 305968 Substitution T A
305885 305886 Substitution CA TC
305880 305880 Substitution T G
305828 305828 Substitution A G
305710 305710 Insertion A
A single nucleotide insertion and several different substitutions were made in the intergenic region between ORFs ALD5/YER073W and RPS24A/YER074W.
New    305701  CAAAAAAAAAAAAACAAAACAAAAAAATAATAACGTGATAAACATTAATGAACAATGTAT  305760
               ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Old    305698  CAAAAAAAAAAAA-CAAAACAAAAAAATAATAACGTGATAAACATTAATGAACAATGTAT  305756
New    305821  TATTGTATATTGAAATATATAGTAATCAAATTCGTTTCATTGATCAAATTGCTCACTAGT  305880
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Old    305817  TATTGTATATTAAAATATATAGTAATCAAATTCGTTTCATTGATCAAATTGCTCACTAGT  305876
New    305881  TCTGTTTTTCAAAATTTCATCTTTATAGGTAGATACAAGTGCCAGAGAGATATATAAACA  305940
               ||| ||||  ||||||||||||||||||||||||||||||||||||||||||||||||||
Old    305877  TCTTTTTTCAAAAATTTCATCTTTATAGGTAGATACAAGTGCCAGAGAGATATATAAACA  305936
New    305941  GAAAACTCTATCGATGTGATAATGTATGCCAATATCGGGACTGTACACCCACACATTTAC  306000
               ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Old    305937  GAAAACTCTATCGATGTGATAATGTATGCCATTATCGGGACTGTACACCCACACATTTAC  305996

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2011-02-03 ARS504 9168 9168 Substitution G T
A single nucleotide substitution was made within ARS504.
New    9121    GTTGGCCTGCCATACTTTAATTGAATAAAAGCTCCGTATATGCTTCTTAAAAATAAGCAA  9180
               ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old    9121    GTTGGCCTGCCATACTTTAATTGAATAAAAGCTCCGTATATGCTTCTGAAAAATAAGCAA  9180

Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98.
SGD paper | PubMed | Full-Text

2000-03-16 YER123W 406383 406383 Deletion G
A single G nucleotide was deleted within ORF YER123W at chromosomal coordinate 406383, creating a new stop codon; this ORF is shortened, but a prenylation site is created.
Old: 406381 TGGATAAAGCGATTTTTATACTTTTCTCTTTTTCCTTTTTTTTTTTGATTGGCTGTTTCC 406440
            || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
New: 406381 TG-ATAAAGCGATTTTTATACTTTTCTCTTTTTCCTTTTTTTTTTTGATTGGCTGTTTCC 406439

Wang X, et al. (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85.
SGD paper | PubMed | Full-Text



Annotation Changes without sequence changes

Date Affected Features
2014-11-19 ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523

As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome V based on Liachko et al. 2013: ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523.

Liachko I, et al. (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704.
SGD paper | PubMed | Full-Text

2014-11-19 ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523

The chromosomal coordinates of the following ARS elements on Chromosome V were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523.

Liachko I, et al. (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704.
SGD paper | PubMed | Full-Text

2014-11-19 ARS513.5, ARS513.7

The following new ARS elements on Chromosome V were added to the genome annotation based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS513.5, ARS513.7.

Liachko I, et al. (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704.
SGD paper | PubMed | Full-Text

2014-11-18 YER109C

The feature_type annotation of FLO8/YER109C was changed from ORF to blocked_reading_frame (SO:0000718) as part of SGD's genome annotation revision R64.2.

2014-07-18 YER038W-A

ORF YER038W-A was upgraded from 'Dubious' to 'Uncharacterized' on 2014-01-30 because its protein product was found in the mitochondria in both the Sickmann et al 2003 and Reinders et al 2006 studies.

Sickmann A, et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12.
SGD paper | PubMed | Full-Text | Web Supplement | YFGdb
Reinders J, et al. (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54.
SGD paper | PubMed | Full-Text | Web Supplement | YFGdb

2007-07-09 YEL003W

The start of GIM4/YEL003W was moved 52 nt upstream, and an intron was added at relative coordinates 20-107, based on GenBank EF123144, Juneau et al. 2007, and Miura et al. 2006. According to Juneau et al. 2007, the intron is "inefficiently spliced" (splicing rate = 72%). The old coding coordinates were 148227..148598 (372 nt, 123 aa), and the new coding coordinates are 148175..148193,148282..148598 (1..19,108..424; 111 aa).

Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51.
SGD paper | PubMed | Full-Text
Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.

2007-04-04 YER131W

RPS26B/YER131W mRNA contains an intron in the 5' untranslated region (UTR).

Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement
Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51.
SGD paper | PubMed | Full-Text
Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.

2007-04-04 YER102W

RPS8B/YER102W mRNA contains an intron in the 5' untranslated region (UTR).

Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement
Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51.
SGD paper | PubMed | Full-Text
Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7.

2007-04-03 YERCdelta8

YERCdelta8, a Ty1 LTR on Chromosome V, was mistakenly annotated on the wrong strand (i.e., on Watson instead of Crick). The error has now been corrected.

2006-10-02 ARS516

The coordinates of ARS516 were updated based on Nieduszynski et al. 2006.

Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9.
SGD paper | PubMed | Full-Text | Web Supplement

2006-09-07 ARS507, ARS508, ARS510, ARS511, ARS512, ARS514, ARS517, ARS518, ARS522

The coordinates of the following ARS elements on Chromosome V were updated based on Nieduszynski et al. 2006: ARS507, ARS508, ARS510, ARS511, ARS512, ARS514, ARS517, ARS518, ARS522/501.

Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9.
SGD paper | PubMed | Full-Text | Web Supplement

2006-05-09 YEL038W

The proposal by Kellis et al. was re-examined in light of sequence data from S. kudriavzevii (another sensu stricto strain published by Cliften et al.). The S. kudriavzevii sequence supported the start codon suggested by Kellis et al., so the start site for UTR4/YEL038W be moved 42 nt (14 codons) downstream.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2006-05-08 CEN5

The previously annotated boundaries of CEN5 were adjusted to coincide with the 5' end of CDEI and the 3' end of CDEIII, to more accurately reflect current knowledge regarding centromere structure in Saccharomyces cerevisiae.

Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60.
SGD paper | PubMed | Full-Text
Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68.
SGD paper | PubMed | Full-Text

2005-11-29 snR80

New snoRNA added to genome annotation.

Schattner P, et al. (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 32(14):4281-96.
SGD paper | PubMed | Full-Text

2005-11-29 YER030W

The start site of YER030W is being moved 21 bp downstream from 213415 to 213436 because the 5' SAGE data used by Zhang & Dietrich 2005 to study transcription start sites confirmed the initial suggestion by Kellis et al. 2003 that this change be made. The size of the predicted protein is reduced from 160 aa to 153 aa.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51.
SGD paper | PubMed | Full-Text | YFGdb

2005-11-28 YER050C

The start site of RSM18/YER050C is being moved 192 bp downstream from 254578 to 254386, based on 5' SAGE data used by Zhang & Dietrich 2005 to study transcription start sites.

Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51.
SGD paper | PubMed | Full-Text | YFGdb

2004-10-19 ARS502, ARS503, ARS504, ARS50, ARS508, ARS510, ARS511, ARS512, ARS513, ARS514, ARS515, ARS516, ARS517, ARS518, ARS519, ARS520, ARS521, ARS522, ARS523

The following ARS elements on Chromosome V were added to SGD based on Tanaka et al. 1996 and Raghuraman et al. 2001: ARS502, ARS503, ARS504, ARS507, ARS508, ARS510, ARS511, ARS512, ARS513, ARS514, ARS515, ARS516, ARS517, ARS518, ARS519, ARS520, ARS521, ARS522, ARS523.

Tanaka S, et al. (1996) Systematic mapping of autonomously replicating sequences on chromosome V of Saccharomyces cerevisiae using a novel strategy. Yeast 12(2):101-13.
SGD paper | PubMed | Full-Text
Raghuraman MK, et al. (2001) Replication dynamics of the yeast genome. Science 294(5540):115-21.
SGD paper | PubMed | Full-Text

2004-10-12 CEN5

Centromeric DNA elements CDEI, CDEII, and CDEIII were annotated based on Wieland et al. 2001 and Espelin et al. 2003.

Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60.
SGD paper | PubMed | Full-Text
Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68.
SGD paper | PubMed | Full-Text

2004-10-08 SCR1

The coordinates of the small cytoplasmic RNA SCR1 were corrected to match the sequence determined by Felici, et al. and reported in the GenBank entry M28116.

Felici F, et al. (1989) The most abundant small cytoplasmic RNA of Saccharomyces cerevisiae has an important function required for normal cell growth. Mol Cell Biol 9(8):3260-8.
SGD paper | PubMed | Full-Text

2004-08-27 YER090C-A

The ORF YER090C-A was added per Oshiro et al. 2002.

Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20.
SGD paper | PubMed | Full-Text | Web Supplement | YFGdb

2004-04-01 RUF4

Feature annotation removed per John McCutcheon and Sean Eddy.

McCutcheon JP and Eddy SR (2004) Detailed correction to: Computational identification of noncoding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res. 31:4119-4128, 2003.
SGD paper | PubMed | Full-Text

2004-01-08 YER074W-A

Both introns in YER074W-A were extended 1 bp in the 5' direction and 2 bp in the 3' direction based on conserved splice site sequences in other fungal species as predicted by Blandin et al. 2000.

Blandin G, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett 487(1):31-6.
SGD paper | PubMed | Full-Text

2003-10-29 SRG1

This non-coding RNA feature was annotated based on information from Fred Winston; the SRG1 TATA begins at position 322124, the transcription start sites are at positions 322208 and 322209, and the size of the transcript is approximately 550 bases as determined by Northern analysis.

2003-09-22 YER178W

Based on the automated comparison of closely-related Saccharomyces species by Kellis et al., the start site for PDA1/YER178W was moved 69 nt (23 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine; 3) The predicted protein translated from the conserved methionine contains a predicted mitochondrial targeting signal sequence (using both MitoProt and Predotar), while the predicted protein translated from the currently annotated S. cerevisiae start codon does not.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2003-09-22 YER032W

Based on the automated comparison of closely-related Saccharomyces species by Kellis et al., the start site for FIR1/YER032W was moved 147 nt (49 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2003-09-22 YER083C

Based on the automated comparison of closely-related Saccharomyces species by Kellis et al., the start site for YER083C was moved 66 nt (22 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2003-09-22 YEL062W

Based on the automated comparison of closely-related Saccharomyces species by Kellis et al., the start site for NPR2/YEL062W was moved 27 nt (9 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2003-09-22 YEL061C

Based on the automated comparison of closely-related Saccharomyces species by Kellis et al., the start site for CIN8/YEL061C was moved 114 nt (38 codons) downstream. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54.
SGD paper | PubMed | Full-Text | Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6.
SGD paper | PubMed | Full-Text | Web Supplement

2003-09-22 TEL05L, TEL05R

The chromosomal locations for the following telomeric elements on Chromosome V were generously provided by Ed Louis and Dave Barton (University of Leicester, UK): TEL05L, TEL05L-XC, TEL05L-YP, TEL05R, TEL05R-XC, TEL05R-XR, TEL05R-YP.

Note that both TEL05L and TEL05R have telomeric repeats (TEL05L-TR and TEL05R-TR), but they are missing from the genome annotation due to sequencing difficulties encountered during the initial genome sequencing efforts in the 1990s.

2003-07-29 YEL009C-A, YEL018C-A, YEL034C-A, YEL053W-A, YER006C-A, YER038W-A, YER046W-A, YER067C-A, YER068C-A, YER076W-A, YER079C-A, YER084W-A, YER087C-A, YER088C-A, YER107W-A, YER133W-A, YER137W-A, YER145C-A, YER147C-A, YER148W-A, YER152W-A, YER165C-A, YER172C-A, YER188C-A

The coordinates for the following ORFs on Chromosome V were provided by MIPS: YEL009C-A, YEL018C-A, YEL034C-A, YEL053W-A, YER006C-A, YER038W-A, YER046W-A, YER067C-A, YER068C-A, YER076W-A, YER079C-A, YER084W-A, YER087C-A, YER088C-A, YER107W-A, YER133W-A, YER137W-A, YER145C-A, YER147C-A, YER148W-A, YER152W-A, YER165C-A, YER172C-A, YER188C-A.

2003-07-29 YEL008C-A, YEL030C-A, YEL032C-A, YEL077W-A, YER023C-A, YER088W-B, YER158W-A, YER175W-A, YER190C-A, YER190C-B

The coordinates for the following ORFs on Chromosome V were provided by Kumar et al. 2002: YEL008C-A, YEL030C-A, YEL032C-A, YEL077W-A, YER023C-A, YER088W-B, YER158W-A, YER175W-A, YER190C-A, YER190C-B.

Kumar A, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63.
SGD paper | PubMed | Full-Text | YFGdb | Comments & Errata

2003-07-29 YEL020C-B, YEL050W-A, YER078W-A

The coordinates for the following ORFs on Chromosome V were provided by Kessler et al. 2003: YEL020C-B, YEL050W-A, YER078W-A.

Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71.
SGD paper | PubMed | Full-Text

2003-03-07 YER180C-A

ORF YER180C-A was added to SGD based on Panic et al. 2003.

Panic B, et al. (2003) The ARF-like GTPases Arl1p and Arl3p act in a pathway that interacts with vesicle-tethering factors at the Golgi apparatus. Curr Biol 13(5):405-10.
SGD paper | PubMed | Full-Text | Comments & Errata

2003-03-06 RUF4

Thanks to John McCutcheon and Sean Eddy for providing the coordinates for the following RNA features: SNR82, SNR83, SNR84, RUF4, RUF5-1, RUF5-2, RUF6, RUF7, and RUF8.

McCutcheon JP and Eddy SR (2003) Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 31(14):4119-28.
SGD paper | PubMed | Full-Text

2002-11-19 YERCTy1-1, YERWdelta18

The YERWdelta18 element was initially mistakenly annotated as a separate LTR, though its coordinates completely overlapped with the full length transposon https://www.yeastgenome.org/locus/YERCTy1-1 YERCTy1-1]. Thus, YERWdelta18 has been deleted from the database.

2002-11-19 YERCTy1-2, YERCsigma4

The YERCsigma4 element was initially mistakenly annotated as a separate sigma LTR, though its coordinates completely overlapped with the full length transposon YERCTy1-2, which contains delta elements, not sigma elements. Thus, YERCsigma4 has been deleted from the genome annotation.

2000-12-01 YER056C-A

The intron of YER056C-A was moved 2 nucleotides upstream. The genomic sequence remains unchanged, but the coding sequence is now only very slightly altered. Relative coordinates change from 1-39..437-763 to 1-37..435-780, and chromosomal coordinates change from 270183-270145..269747-269421 to 270183-270147..269749-269421.

2000-12-01 YEL012W

The start site of YEL012W was moved 159 nucleotides upstream, and an intron was added at relative coordinates 6-128. The stop remains unchanged. Relative coordinates change from 1-621 to 1-5..129-780, and chromosomal coordinates change from 131931-132551 to 131772-131776..131900-132551.

1999-07-17 YER060W-A

YER060W-A/FCY22 was originally incorrectly annotated as being identical to its neighboring ORF YER060W/FCY21, at coordinates 274565-276151 (1587 nucleotides long). This error has been corrected, and the coordinates of YER060W-A/FCY22 are now 276570-278162 (1593 nt). Sequence files have been updated accordingly.

1999-07-17 YER108C, YER109C

YER108C and YER109C were originally annotated as two separate open reading frames, but it has been demonstrated that they correspond to the FLO8 gene, which contains a nonsense mutation in the reference strain S288C - an A to G transition at position 431, changing amino acid 144 from a Trp to a stop. Therefore, they have been fused into one reading frame with an internal stop codon.

Liu H, et al. (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144(3):967-78.
SGD paper | PubMed | Full-Text

1998-05-21 YER048W-A, YER091C-A, YER138W-A

The following 27 ORFs were added to the genome annotation based on Velculescu et al. 1997: YBL091C-A, YBL107W-A, YCR018C-A, YCR102W-A, YDL130W-A, YDR034C-A, YDR034W-B, YDR363W-A, YDR525W-A, YER048W-A, YER091C-A, YER138W-A, YGR122C-A, YIR020W-B, YKL033W-A, YKL053C-A, YKL162C-A, YLL018C-A, YLR262C-A, YML081C-A, YMR046W-A, YMR158C-B, YMR194C-A, YNR032C-A, YOL013W-A, YOR298C-A, and YPR002C-A.

The coordinates of the tag sequences along the genome were determined and each tag was classified into one of these four categories: 1) class 1 - within an existing ORF, 2) class 2 - within 500 bp downstream of existing an ORF, 3) class 4 - opposite of an existing ORF, or 4) class 3 - none of the above. The regions between two existing ORFs which contained one or more unique class 3 tags (number 4) above) were examined for potential coding sequences in which the unique tag was located either within the coding sequence or 500bp downstream of this sequence. BLASTP analysis was then performed for each potential ORF meeting these criteria against the non-redundant (nr) NCBI dataset, and those with a P value exponent of -6 or less were analyzed further. The BLAST results were analyzed on an individual basis for each potential ORF meeting the above criteria. Those potential ORFs which exhibited reasonable homology to other proteins, and did not appear to be matched with other proteins based on homology to repetitive sequences alone, were identified and entered into SGD.

Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51.
SGD paper | PubMed | Full-Text | YFGdb