Chromosome VIII History - Revision history

Stacia at 22:08, 21 April 2022

2022-04-21T22:08:01Z

Stacia: /* Annotation Changes without sequence changes */

2022-04-21T21:06:46Z

‎Annotation Changes without sequence changes

Sage at 15:58, 1 October 2019

2019-10-01T15:58:01Z

Sage at 19:57, 30 September 2019

2019-09-30T19:57:24Z

Sage: /* Annotation Changes without sequence changes */

2019-09-30T19:57:03Z

‎Annotation Changes without sequence changes

Sage at 19:30, 30 September 2019

2019-09-30T19:30:20Z

Sage: /* Annotation Changes without sequence changes */

2019-09-30T19:19:40Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-09-30T19:14:37Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-09-30T19:05:45Z

‎Annotation Changes without sequence changes

Sage at 18:44, 30 September 2019

2019-09-30T18:44:34Z

@@ Line 1: / Line 1: @@
 This page lists all sequence and annotation changes that have been made to the Chromosome VIII systematic reference sequence since its intial release on 1996-07-31. <br>
 *The sequence of Chromosome VIII has been updated '''33''' times, affecting '''40''' features. <br>
-*The annotation of Chromosome VIII has been updated '''24''' times, affecting '''69''' features. <br>
+*The annotation of Chromosome VIII has been updated '''27''' times, affecting '''72''' features. <br>
 *Current and past versions can be obtained from SGD's [https://www.yeastgenome.org/downloads Download site].

@@ Line 519: / Line 519: @@
 {| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
 ! Date  !! Affected Features
 |-
 | 2014-11-19

@@ Line 1: / Line 1: @@
 This page lists all sequence and annotation changes that have been made to the Chromosome VIII systematic reference sequence since its intial release on 1996-07-31. <br>
-*The sequence of Chromosome VII has been updated '''33''' times, affecting '''40''' features. <br>
+*The sequence of Chromosome VIII has been updated '''33''' times, affecting '''40''' features. <br>
-*The annotation of Chromosome VII has been updated '''24''' times, affecting '''69''' features. <br>
+*The annotation of Chromosome VIII has been updated '''24''' times, affecting '''69''' features. <br>
 *Current and past versions can be obtained from SGD's [https://www.yeastgenome.org/downloads Download site].

← Older revision		Revision as of 19:57, 30 September 2019
Line 685:		Line 685:
	\| [https://www.yeastgenome.org/locus/YHR079C-A YHR079C-A]<br>		\| [https://www.yeastgenome.org/locus/YHR079C-A YHR079C-A]<br>
	Old name: YHR079C-B; new name: YHR079C-A; date: 11/1998; old coord: ChrVIII 262554 262402; SGDID: S0001957; Name changed due to nomenclature.<br><br>		Old name: YHR079C-B; new name: YHR079C-A; date: 11/1998; old coord: ChrVIII 262554 262402; SGDID: S0001957; Name changed due to nomenclature.<br><br>
		+
		+	\|}

← Older revision		Revision as of 19:57, 30 September 2019
Line 625:		Line 625:
	'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <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>		[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/YHR064C YHR064C]<br>
		+	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for SSZ1/YHR064C be moved 102 nt (34 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. 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) protein sequence conservation with other chaperone homologs in S. cerevisiae begins sharply at about 30 amino acids from the current start.<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/YHR128W YHR128W]<br>
		+	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for FUR1/YHR128W be moved 106 nt (35 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. 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>
		+	\|-
		+	\| 2003-09-09
		+	\| [https://www.yeastgenome.org/locus/TEL08L TEL08L], [https://www.yeastgenome.org/locus/TEL08R TEL08R]<br>
		+	The chromosomal locations for TEL08L, TEL08L-TR, TEL08L-XC, TEL08L-XR, TEL08L-YP, TEL08R, TEL08R-TR1 , TEL08R-TR2, TEL08R-XC, TEL08R-XR, and TEL08R-YP were generously provided by Ed Louis and Dave Barton (University of Leicester, UK).<br><br>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YHL015W-A YHL015W-A], [https://www.yeastgenome.org/locus/YHL048C-A YHL048C-A], [https://www.yeastgenome.org/locus/YHR007C-A YHR007C-A], [https://www.yeastgenome.org/locus/YHR032W-A YHR032W-A], [https://www.yeastgenome.org/locus/YHR050W-A YHR050W-A], [https://www.yeastgenome.org/locus/YHR073C-B YHR073C-B], [https://www.yeastgenome.org/locus/YHR073W-A YHR073W-A]<br>
		+	Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome VIII ORFs: YHL015W-A, YHL048C-A, YHR007C-A, YHR032W-A, YHR050W-A, YHR073C-B, and YHR073W-A.<br><br>
		+	'''Basrai MA, et al.''' (1999) NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae. Mol Cell Biol 19(10):7041-9. <br>
		+	[https://www.yeastgenome.org/reference/S000042214 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10490641 PubMed] \| [https://mcb.asm.org/content/19/10/7041.long Full-Text] <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>
		+	'''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>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YHL002C-A YHL002C-A], [https://www.yeastgenome.org/locus/YHL006W-A YHL006W-A], [https://www.yeastgenome.org/locus/YHL019W-A YHL019W-A], [https://www.yeastgenome.org/locus/YHL030W-A YHL030W-A], [https://www.yeastgenome.org/locus/YHL034W-A YHL034W-A], [https://www.yeastgenome.org/locus/YHL046W-A YHL046W-A], [https://www.yeastgenome.org/locus/YHR028W-A YHR028W-A], [https://www.yeastgenome.org/locus/YHR056W-A YHR056W-A], [https://www.yeastgenome.org/locus/YHR063W-A YHR063W-A], [https://www.yeastgenome.org/locus/YHR069C-A YHR069C-A], [https://www.yeastgenome.org/locus/YHR070C-A YHR070C-A], [https://www.yeastgenome.org/locus/YHR071C-A YHR071C-A], [https://www.yeastgenome.org/locus/YHR131W-A YHR131W-A], [https://www.yeastgenome.org/locus/YHR165W-A YHR165W-A], [https://www.yeastgenome.org/locus/YHR182C-A YHR182C-A], [https://www.yeastgenome.org/locus/YHR193C-A YHR193C-A], [https://www.yeastgenome.org/locus/YHR218W-A YHR218W-A]<br>
		+	Thanks to [https://bioinformatik.wzw.tum.de/index.php?id=63 MIPS] for providing the coordinates for the following Chromosome VIII ORFs: YHL002C-A, YHL006W-A, YHL019W-A, YHL030W-A, YHL034W-A, YHL046W-A, YHR028W-A, YHR032C-A, YHR056W-A, YHR063W-A, YHR069C-A, YHR070C-A, YHR071C-A, YHR131W-A, YHR165W-A, YHR182C-A, YHR193C-A, and YHR218W-A.<br><br>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YHR086W-A YHR086W-A], [https://www.yeastgenome.org/locus/YHR175W-A YHR175W-A], [https://www.yeastgenome.org/locus/YHR180C-B YHR180C-B], [https://www.yeastgenome.org/locus/YHR180W-A YHR180W-A]<br>
		+	Thanks to Kessler et al. for providing the coordinates of the following Chromosome VIII ORFs: YHR180C-B, YHR180W-A, YHR175W-A, and YHR086W-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>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YHL050W-A YHL050W-A], [https://www.yeastgenome.org/locus/YHR022C-A YHR022C-A], [https://www.yeastgenome.org/locus/YHR032C-A YHR032C-A], [https://www.yeastgenome.org/locus/YHR052W-A YHR052W-A], [https://www.yeastgenome.org/locus/YHR054W-A YHR054W-A], [https://www.yeastgenome.org/locus/YHR137C-A YHR137C-A], [https://www.yeastgenome.org/locus/YHR212W-A YHR212W-A], [https://www.yeastgenome.org/locus/YHR213W-A YHR213W-A], [https://www.yeastgenome.org/locus/YHR213W-B YHR213W-B], [https://www.yeastgenome.org/locus/YHR214C-D YHR214C-D], [https://www.yeastgenome.org/locus/YHR214C-E YHR214C-E], [https://www.yeastgenome.org/locus/YHR219C-A YHR219C-A]<br>
		+	Thanks to Kumar et al. for providing the coordinates of the followinc Chromosome VIII ORFs: YHL050W-A, YHR052W-A, YHR137C-A, YHR213W-A, YHR213W-B, YHR214C-D, YHR214C-E, YHR219C-A, YHR212W-A, YHR054W-A, YHR032C-A, and YHR022C-A.<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>
		+	\|-
		+	\| 2003-03-06
		+	\| [https://www.yeastgenome.org/locus/RUF5-1 RUF5-1], [https://www.yeastgenome.org/locus/RUF5-2 RUF5-2]<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>
		+	\|-
		+	\| 2000-08-11
		+	\| [https://www.yeastgenome.org/locus/YHR039C-A YHR039C-A]<br>
		+	Old name: YHR039C-B; new name: YHR039C-A; date: 11/1998; old coord: ChrVIII 187670 187164; SGDID: S0002100; Name changed due to nomenclature.<br><br>
		+	\|-
		+	\| 2000-08-11
		+	\| [https://www.yeastgenome.org/locus/YHR079C-A YHR079C-A]<br>
		+	Old name: YHR079C-B; new name: YHR079C-A; date: 11/1998; old coord: ChrVIII 262554 262402; SGDID: S0001957; Name changed due to nomenclature.<br><br>

← Older revision		Revision as of 19:30, 30 September 2019
Line 597:		Line 597:
	'''Tsubouchi H and Roeder GS''' (2002) The Mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Mol Cell Biol 22(9):3078-88. <br>		'''Tsubouchi H and Roeder GS''' (2002) The Mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Mol Cell Biol 22(9):3078-88. <br>
	[https://www.yeastgenome.org/reference/S000069966 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11940665 PubMed] \| [https://mcb.asm.org/content/22/9/3078 Full-Text] <br>		[https://www.yeastgenome.org/reference/S000069966 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11940665 PubMed] \| [https://mcb.asm.org/content/22/9/3078 Full-Text] <br>
		+	\|-
		+	\| 2004-10-12
		+	\| [https://www.yeastgenome.org/locus/CEN8 CEN8]<br>
		+	The orientation of this centromere was reversed (from Watson to Crick) to accommodate annotation of the centromeric DNA elements CDEI, CDEII, and CDEIII based on Wieland et al. and Espelin et al.<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>
		+	\|-
		+	\| 2004-04-01
		+	\| [https://www.yeastgenome.org/locus/RUF5-1 RUF5-1], [https://www.yeastgenome.org/locus/RUF5-2 RUF5-2]<br>
		+	Start and stop coordinates updated per McCutcheon & Eddy 2004.<br><br>
		+	'''McCutcheon JP and Eddy SR''' (2004) GDetailed 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>
		+	\|-
		+	\| 2004-02-20
		+	\| [https://www.yeastgenome.org/locus/YHR199C-A YHR199C-A]<br>
		+	Thanks to Cliften et al. for providing the coordinates of YHR199C-A.<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>
		+	\|-
		+	\| 2003-09-22
		+	\| [https://www.yeastgenome.org/locus/YHR065C YHR065C]<br>
		+	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for RRP3/YHR065C be moved 126 nt (42 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. 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>

← Older revision		Revision as of 19:19, 30 September 2019
Line 574:		Line 574:
	'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>		'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>
	[https://www.yeastgenome.org/reference/S000069019 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] \| [https://www.pnas.org/content/84/22/8035.long Full-Text]<br>		[https://www.yeastgenome.org/reference/S000069019 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] \| [https://www.pnas.org/content/84/22/8035.long Full-Text]<br>
		+	\|-
		+	\| 2005-11-07
		+	\| [https://www.yeastgenome.org/locus/YHR163W YHR163W]<br>
		+	High-throughput identification of transcription start sites by Zhang and Dietrich 2005 confirmed that the start site for YHR163W should be moved 93 nt downstream from 423632 to 423725. As a consequence of this annotation change, YHR163W was shortened at the 5' end, decreasing the size of the predicted protein from 280 amino acids to 249 amino acids.<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>
		+	\|-
		+	\| 2005-11-03
		+	\| [https://www.yeastgenome.org/locus/YHR079C-A YHR079C-A]<br>
		+	The following intron predicted by Brachat, et al was added to SAE3/YHR079C-A on the basis of experimental evidence provided by Hayase, et al and Tsubouchi and Roeder:
		+	exon 1: ...tgtctaaaga aaagaaaaa<br> <br>
		+	<pre>intron: g tatgtagcta ttttttccag tcggcaaaaa tcggtataac aaacaaaaaa tatttagttt ctgttattaa cagaacttgt caaag
		+
		+	exon2: tgatg agacaccaaa aaaaatttcc tcgacgtaca ttaaagagtt...</pre>
		+	<br>
		+	'''Brachat S, et al.''' (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45. <br>
		+	[https://www.yeastgenome.org/reference/S000073670 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12844361 PubMed] \| [https://genomebiology.biomedcentral.com/articles/10.1186/gb-2003-4-7-r45 Full-Text] <br>
		+	'''Hayase A, et al.''' (2004) A protein complex containing Mei5 and Sae3 promotes the assembly of the meiosis-specific RecA homolog Dmc1. Cell 119(7):927-40. <br>
		+	[https://www.yeastgenome.org/reference/S000080355 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/15620352 PubMed] \| [https://www.sciencedirect.com/science/article/pii/S0092867404011420?via%3Dihub Full-Text] <br>
		+	'''Tsubouchi H and Roeder GS''' (2002) The Mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Mol Cell Biol 22(9):3078-88. <br>
		+	[https://www.yeastgenome.org/reference/S000069966 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11940665 PubMed] \| [https://mcb.asm.org/content/22/9/3078 Full-Text] <br>

← Older revision		Revision as of 19:14, 30 September 2019
Line 558:		Line 558:
	'''Nieduszynski CA, et al.''' (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. <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>		[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>
		+	\|-
		+	\| 2006-04-13
		+	\| [https://www.yeastgenome.org/locus/ARS808 ARS808]<br>
		+	ARS808, also known as ARS2, was added to the genome annotation for Chromosome VII at coordinates 140342-141267 based on Wyrick et al. 2001 and Hsiao & Carbon 1981. "ARS2" is being retained as the Standard Gene Name for historical reasons, but the systematic name "ARS808" is being used for consistency purposes, to indicate that this ARS is part of Chromosome VIII.<br> <br>
		+	'''Hsiao CL and Carbon J''' (1981) Characterization of a yeast replication origin (ars2) and construction of stable minichromosomes containing cloned yeast centromere DNA (CEN3). Gene 15(2-3):157-66. <br>
		+	[https://www.yeastgenome.org/reference/S000041563 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/7028571 PubMed] \| [https://www.sciencedirect.com/science/article/pii/0378111981901256?via%3Dihub Full-Text]<br>
		+	'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>
		+	[https://www.yeastgenome.org/reference/S000069019 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] \| [https://science.sciencemag.org/content/294/5550/2357.long Full-Text] \| [https://www.ncbi.nlm.nih.gov/pubmed/11743187 Comments & Errata]<br>
		+	\|-
		+	\| 2006-04-13
		+	\| [https://www.yeastgenome.org/locus/ARS805 ARS805]<br>
		+	ARS805, also known as "SPO11 ARS", was added to the genome annotation for Chromosome VIII at coordinates 64155-64459 based on Wyrick et al. 2001 and Atcheson et al. 1987.<br> <br>
		+	'''Atcheson CL, et al.''' (1987) Isolation, DNA sequence, and regulation of a meiosis-specific eukaryotic recombination gene. Proc Natl Acad Sci U S A 84(22):8035-9. <br>
		+	[https://www.yeastgenome.org/reference/S000053823 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/3317399 PubMed] \| [https://www.sciencedirect.com/science/article/pii/0378111981901256?via%3Dihub Full-Text]<br>
		+	'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>
		+	[https://www.yeastgenome.org/reference/S000069019 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] \| [https://www.pnas.org/content/84/22/8035.long Full-Text]<br>

← Older revision		Revision as of 19:05, 30 September 2019
Line 519:		Line 519:
	{\| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"		{\| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
	! Date !! Affected Features		! Date !! Affected Features
		+	\|-
		+	\| 2014-11-19
		+	\| [https://www.yeastgenome.org/locus/ARS802 ARS802], [https://www.yeastgenome.org/locus/ARS805 ARS805], [https://www.yeastgenome.org/locus/ARS807 ARS807], [https://www.yeastgenome.org/locus/ARS813 ARS813], [https://www.yeastgenome.org/locus/ARS818 ARS818], [https://www.yeastgenome.org/locus/ARS820 ARS820]<br>
		+	As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome VIII based on Liachko et al. 2013: ARS802, ARS805, ARS807, ARS813, ARS818, ARS820.<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/ARS802 ARS802], [https://www.yeastgenome.org/locus/ARS805 ARS805], [https://www.yeastgenome.org/locus/ARS807 ARS807], [https://www.yeastgenome.org/locus/ARS809 ARS809], [https://www.yeastgenome.org/locus/ARS813 ARS813], [https://www.yeastgenome.org/locus/ARS815 ARS815], [https://www.yeastgenome.org/locus/ARS818 ARS818], [https://www.yeastgenome.org/locus/ARS820 ARS820]<br>
		+	The chromosomal coordinates of the following ARS elements on Chromosome VIII were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS802, ARS805, ARS807, ARS809, ARS813, ARS815, ARS818, ARS820.<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]
		+	\|-
		+	\| 2009-05-06
		+	\| [https://www.yeastgenome.org/locus/ARS801 ARS801], [https://www.yeastgenome.org/locus/ARS806 ARS806], [https://www.yeastgenome.org/locus/ARS810 ARS810], [https://www.yeastgenome.org/locus/ARS811 ARS811], [https://www.yeastgenome.org/locus/ARS814 ARS814], [https://www.yeastgenome.org/locus/ARS815 ARS815] <br>
		+	The following ARS elements on Chromosome 8 were added to the genome annotation based on Raveendranathan et al. 2006: ARS801, ARS806, ARS810, ARS811, ARS814, and ARS815.<br> <br>
		+	'''Raveendranathan M, et al.''' (2006) Genome-wide replication profiles of S-phase checkpoint mutants reveal fragile sites in yeast. EMBO J 25(15):3627-39. <br>
		+	[https://www.yeastgenome.org/reference/S000117571 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/16888628 PubMed] \| [https://www.embopress.org/cgi/doi/10.1038/sj.emboj.7601251 Full-Text]
		+	\|-
		+	\| 2007-07-09
		+	\| [https://www.yeastgenome.org/locus/YHR076W YHR076W] <br>
		+	An intron was annotated within PTC7/YHR076W at relative coordinates 56..148 based on GenBank EF123135, Juneau et al. 2007, and Zhang et al. 2007. According to Juneau et al. 2007, the intron is "inefficiently spliced" (splicing rate = 55%). Note that the currently annotated start and stop remain the same.<br> <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>
		+	[https://www.yeastgenome.org/reference/S000120506 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17244705 PubMed] \| [https://www.pnas.org/content/104/5/1522.long Full-Text] <br>
		+	'''Zhang Z, et al.''' (2007) Genome-wide identification of spliced introns using a tiling microarray. Genome Res 17(4):503-9. <br>
		+	[https://www.yeastgenome.org/reference/S000121920 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17351133 PubMed] \| [https://genome.cshlp.org/content/17/4/503 Full-Text] \| [http://yfgdb.princeton.edu/cgi-bin/display.cgi?id=17351133&db=pmid YFGdb]
		+	\|-
		+	\| 2006-09-07
		+	\| [https://www.yeastgenome.org/locus/ARS802 ARS802], [https://www.yeastgenome.org/locus/ARS807 ARS807], [https://www.yeastgenome.org/locus/ARS809 ARS809], [https://www.yeastgenome.org/locus/ARS813 ARS813], [https://www.yeastgenome.org/locus/ARS818 ARS818], [https://www.yeastgenome.org/locus/ARS820 ARS820], [https://www.yeastgenome.org/locus/ARS822 ARS822], [https://www.yeastgenome.org/locus/ARS824 ARS824]<br>
		+	The following new ARS elements on Chromosome VIII were added to SGD based on Nieduszynski et al. 2006: ARS802, ARS807, ARS809, ARS813, ARS818, ARS820, ARS822, ARS824.<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/ARS805 ARS805]<br>
		+	The coordinates of ARS805 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>