Chromosome XIV History - Revision history

Stacia at 22:10, 21 April 2022

2022-04-21T22:10:13Z

Stacia: /* Annotation Changes without sequence changes */

2022-04-21T22:04:53Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:52:56Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:51:12Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:40:13Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:38:50Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:36:25Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:15:13Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:10:49Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-02T21:06:51Z

‎Annotation Changes without sequence changes

@@ Line 1: / Line 1: @@
 This page lists all sequence and annotation changes that have been made to the Chromosome XIV systematic reference sequence since its intial release on 1996-07-31. <br>
 *The sequence of Chromosome XIV has been updated '''43''' times, affecting '''41''' features. <br>
-*The annotation of Chromosome XIV has been updated '''33''' times, affecting '''59''' features. <br>
+*The annotation of Chromosome XIV has been updated '''34''' times, affecting '''60''' features. <br>
 *Current and past versions can be obtained from SGD's [https://www.yeastgenome.org/downloads Download site].

@@ Line 635: / Line 635: @@
 {| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
 ! Date  !! Affected Features
 |-
 | 2014-11-19

← Older revision		Revision as of 21:52, 2 October 2019
Line 847:		Line 847:
	'''Davis CA, et al.''' (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res 28(8):1700-6. <br>		'''Davis CA, et al.''' (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res 28(8):1700-6. <br>
	[https://www.yeastgenome.org/reference/S000042737 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10734188 PubMed] \| [https://academic.oup.com/nar/article/28/8/1700/1009222 Full-Text] <br>		[https://www.yeastgenome.org/reference/S000042737 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10734188 PubMed] \| [https://academic.oup.com/nar/article/28/8/1700/1009222 Full-Text] <br>
		+	\|-
		+	\| 1999-11-17
		+	\| [https://www.yeastgenome.org/locus/YNL044W YNL044W]
		+	The start site of YNL044W was moved 133 base pairs upstream and at the same time an intron was added at new relative coordinates 25-103.<br><br>
		+	\|-
		+	\| 1998-05-21
		+	\| [https://www.yeastgenome.org/locus/YNR032C-A YNR032C-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. <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>
		+
		+	\|}

← Older revision		Revision as of 21:51, 2 October 2019
Line 789:		Line 789:
	'''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>
		+	\|-
		+	\| 2003-09-09
		+	\| [https://www.yeastgenome.org/locus/TEL14L TEL14L], [https://www.yeastgenome.org/locus/TEL14R TEL14R]
		+	The chromosomal locations for TEL14L, TEL14L-TR, TEL14L-XC, TEL14L-XR, TEL14L-YP, TEL14R, TEL14R-TR, TEL14R-XC, and TEL14R-XR were generously provided by Ed Louis and Dave Barton (University of Leicester, UK).<br><br>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YNL130C-A YNL130C-A]
		+	Thanks to Kessler et al. for providing the coordinates of YNL130C-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/YNL138W-A YNL138W-A]
		+	Thanks to Brachat et al. and Cliften et al.for providing the coordinates of YNL138W-A.<br><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>
		+	'''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>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YNL024C-A YNL024C-A], [https://www.yeastgenome.org/locus/YNL097C-B YNL097C-B], [https://www.yeastgenome.org/locus/YNL097W-A YNL097W-A], [https://www.yeastgenome.org/locus/YNL103W-A YNL103W-A], [https://www.yeastgenome.org/locus/YNL144W-A YNL144W-A], [https://www.yeastgenome.org/locus/YNL339W-A YNL339W-A], [https://www.yeastgenome.org/locus/YNL339W-B YNL339W-B], [https://www.yeastgenome.org/locus/YNR003W-A YNR003W-A], [https://www.yeastgenome.org/locus/YNR075C-A YNR075C-A]
		+	Thanks to Kumar et al. for providing the coordinates of the following Chromosome XIV ORFs: YNL097C-B, YNL103W-A, YNL339W-A, YNR003W-A, YNR075C-A, YNL339W-B, YNL144W-A, YNL097W-A, and YNL024C-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>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YNL067W-B YNL067W-B]
		+	Thanks to [https://bioinformatik.wzw.tum.de/index.php?id=63 MIPS] for providing the coordinates of YNL067W-B.<br><br>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YNL042W-B YNL042W-B], [https://www.yeastgenome.org/locus/YNL146C-A YNL146C-A], [https://www.yeastgenome.org/locus/YNL277W-A YNL277W-A]
		+	Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome XIV ORFs: YNL042W-B, YNL146C-A, and YNL277W-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>
		+	\|-
		+	\| 2003-02-03
		+	\| [https://www.yeastgenome.org/locus/snR191 snR191]
		+	Previously unmapped small nucleolar RNA feature snR191 was added.<br><br>
		+	\|-
		+	\| 2003-01-07
		+	\| [https://www.yeastgenome.org/locus/YNL239W YNL239W]
		+	Gal6p purified from yeast indicates that native Gal6p is translated from the second translation start codon (454 aa and not 483 aa). Therefore, the start site of LAP3/GAL6/YNL239W has been moved 87 nt downstream from 200481 to 200568.<br><br>
		+	'''Zheng W, et al.''' (1997) The cysteine-peptidase bleomycin hydrolase is a member of the galactose regulon in yeast. J Biol Chem 272(48):30350-5. <br>
		+	[https://www.yeastgenome.org/reference/S000063844 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/9374524 PubMed] \| [http://www.jbc.org/content/272/48/30350.long Full-Text] <br>
		+	\|-
		+	\| 2000-12-01
		+	\| [https://www.yeastgenome.org/locus/YNL162W YNL162W]
		+	The boundary between the intron and the downstream exon of YNL162W was moved 30 base pairs downstream, so that the relative coding coordinates change from 1-4..487-833 to 1-4..517-833.<br><br>
		+	\|-
		+	\| 2000-07-14
		+	\| [https://www.yeastgenome.org/locus/YNL012W YNL012W]
		+	The start site of YNL012W was moved 369 base pairs upstream and at the same time an intron was added at new relative coordinates 106-189.<br><br>
		+	'''Davis CA, et al.''' (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res 28(8):1700-6. <br>
		+	[https://www.yeastgenome.org/reference/S000042737 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10734188 PubMed] \| [https://academic.oup.com/nar/article/28/8/1700/1009222 Full-Text] <br>

@@ Line 761: / Line 761: @@
 | [https://www.yeastgenome.org/locus/YNL223W YNL223W]
 Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for ATG4/YNL223W be moved 36 nt (12 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) The first ATG is not conserved in S. paradoxus, S. mikatae, and S. bayanus; 4) In an independent Genbank record also uses the second ATG for the protein translation (Version AAA86498.1 GI:1173491).<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 21:38, 2 October 2019
Line 751:		Line 751:
	'''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>		'''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>		[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>
		+	\|-
		+	\| 2003-09-27
		+	\| [https://www.yeastgenome.org/locus/YNL038W YNL038W]
		+	Based on the alignment of orthologs in related Saccharomyces species, Cliften et al. proposed an intron and new 3' exon for GPI15/YNL038W. The resulting ORF is 17 residues longer and has an altered C-terminus. This change was reviewed and accepted by SGD curators.<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/YNL223W YNL223W]
		+	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for ATG4/YNL223W be moved 36 nt (12 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) The first ATG is not conserved in S. paradoxus, S. mikatae, and S. bayanus; 4) In an independent Genbank record also uses the second ATG for the protein translation (Version AAA86498.1 GI:1173491).<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 21:36, 2 October 2019
Line 699:		Line 699:
	'''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>
		+	\|-
		+	\| 2006-05-10
		+	\| [https://www.yeastgenome.org/locus/YNL310C YNL310C]
		+	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 ZIM17/YNL310C be moved 93 nt (31 amino acids) 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>
		+	\|-
		+	\| 2006-05-10
		+	\| [https://www.yeastgenome.org/locus/YNL202W YNL202W]
		+	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 SPS19/YNL202W was moved 9 nt (3 amino acids) 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>
		+	\|-
		+	\| 2004-10-18
		+	\| [https://www.yeastgenome.org/locus/ARS1411 ARS1411], [https://www.yeastgenome.org/locus/ARS1412 ARS1412], [https://www.yeastgenome.org/locus/ARS1413 ARS1413], [https://www.yeastgenome.org/locus/ARS1414 ARS1414] <br>
		+	ARS1411, ARS1412, ARS1413, and ARS1414 were added to SGD based on Friedman et al., and Raghuraman et al. <br> <br>
		+	'''Friedman KL, et al.''' (1996) Multiple determinants controlling activation of yeast replication origins late in S phase. Genes Dev 10(13):1595-607. <br>
		+	[https://www.yeastgenome.org/reference/S000064277 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/8682291 PubMed] \| [http://genesdev.cshlp.org/content/10/13/1595.long 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/CEN14 CEN14]
		+	The coordinates of this centromere were updated to accommodate annotation of the centromeric DNA elements CDEI, CDEII, and CDEIII 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>
		+	\|-
		+	\| 2004-04-21
		+	\| [https://www.yeastgenome.org/locus/YNL082W YNL082W]
		+	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for PMS1/YNL082W be moved 93 nt downstream. This suggestion was reviewed by SGD curators and incorporated. Evidence supporting this change includes: 1) This is the predicted start methionine in S. bayanus, S. paradoxus and S. mikatae; 2) The proposed start methionine is conserved in the S. kluyveri, S. castellii, and S. kudriavzevii sequences published by Cliften et al. 3) DNA sequence conservation begins abruptly at this ATG.<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>
		+	\|-
		+	\| 2004-02-04
		+	\| [https://www.yeastgenome.org/locus/snR19 snR19]
		+	Start moved 100 bp downstream from 230771 to 230671. See GenBank M17205, Z71497, and Z71498.<br><br>
		+	\|-
		+	\| 2004-02-03
		+	\| [https://www.yeastgenome.org/locus/YNL130C YNL130C]
		+	Start moved 328 bp downstream based on sequence conservation in other Saccharomyces species. In addition, the 5' splice site for the existing intron moved 349 bp downstream. There is no change to Exon 2.<br><br>
		+	'''Hjelmstad RH and Bell RM''' (1990) The sn-1,2-diacylglycerol cholinephosphotransferase of Saccharomyces cerevisiae. Nucleotide sequence, transcriptional mapping, and gene product analysis of the CPT1 gene. J Biol Chem 265(3):1755-64. <br>
		+	[https://www.yeastgenome.org/reference/S000039137 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/2153142 PubMed] \| [http://www.jbc.org/content/265/3/1755.long Full-Text] <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>

← Older revision		Revision as of 21:15, 2 October 2019
Line 687:		Line 687:
	<br>		<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>		[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>
		+	\|-
		+	\| 2006-09-07
		+	\| [https://www.yeastgenome.org/locus/ARS1405 ARS1405], [https://www.yeastgenome.org/locus/ARS1406 ARS1406], [https://www.yeastgenome.org/locus/ARS1407 ARS1407], [https://www.yeastgenome.org/locus/ARS1415 ARS1415], [https://www.yeastgenome.org/locus/ARS1417 ARS1417], [https://www.yeastgenome.org/locus/ARS1419 ARS1419], [https://www.yeastgenome.org/locus/ARS1420 ARS1420], [https://www.yeastgenome.org/locus/ARS1421 ARS1421], [https://www.yeastgenome.org/locus/ARS1422 ARS1422], [https://www.yeastgenome.org/locus/ARS1424 ARS1424], [https://www.yeastgenome.org/locus/ARS1426 ARS1426], [https://www.yeastgenome.org/locus/ARS1427 ARS1427] <br>
		+	The following new ARS elements on Chromosome XIV were added to SGD based on Nieduszynski et al. 2006: ARS1405, ARS1406, ARS1407, ARS1415, ARS1417, ARS1419, ARS1420, ARS1421, ARS1422, ARS1424, ARS1426, ARS1427. <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/ARS1411 ARS1411], [https://www.yeastgenome.org/locus/ARS1412 ARS1412], [https://www.yeastgenome.org/locus/ARS1414 ARS1414] <br>
		+	The coordinates of the following ARS elements on Chromosome XIV were updated based on Nieduszynski et al. 2006: ARS1411, ARS1412, ARS1414. <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>

← Older revision		Revision as of 21:10, 2 October 2019
Line 661:		Line 661:
	'''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>		'''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]<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]<br>
		+	\|-
		+	\| 2007-09-06
		+	\| [https://www.yeastgenome.org/locus/YNL147W YNL147W]
		+	The 3' end of the intron within LSM7/YNL147W was moved 24 nt upstream, from chromosomal coordinate 351079 to 351055, based on Miura et al. 2006.<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>
		+	\|-
		+	\| 2007-07-09
		+	\| [https://www.yeastgenome.org/locus/YNL004W YNL004W]
		+	The start of ORF HRB1/YNL004W was moved 417 nt upstream and an intron was added at relative coordinates 31..372 based on GenBank EF123128, Juneau et al. 2007, and Zhang et al. 2007. The ORF had been annotated as 1290 nt long, but is now 1707 nt in length.<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]<br>
		+	\|-
		+	\| 2007-04-04
		+	\| [https://www.yeastgenome.org/locus/YNL066W YNL066W]
		+	SUN4/YNL066W 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>
		+	[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>

← Older revision		Revision as of 21:06, 2 October 2019
Line 635:		Line 635:
	{\| 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/ARS1411 ARS1411], [https://www.yeastgenome.org/locus/ARS1412 ARS1412], [https://www.yeastgenome.org/locus/ARS1414 ARS1414], [https://www.yeastgenome.org/locus/ARS1419 ARS1419], [https://www.yeastgenome.org/locus/ARS1420 ARS1420], [https://www.yeastgenome.org/locus/ARS1421 ARS1421], [https://www.yeastgenome.org/locus/ARS1424 ARS1424] <br>
		+	The chromosomal coordinates of the following ARS elements on Chromosome XIV were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS1411, ARS1412, ARS1414, ARS1419, ARS1420, ARS1421, ARS1424. <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/ARS1405 ARS1405], [https://www.yeastgenome.org/locus/ARS1406 ARS1406], [https://www.yeastgenome.org/locus/ARS1407 ARS1407], [https://www.yeastgenome.org/locus/ARS1411 ARS1411], [https://www.yeastgenome.org/locus/ARS1414 ARS1414], [https://www.yeastgenome.org/locus/ARS1415 ARS1415], [https://www.yeastgenome.org/locus/ARS1419 ARS1419], [https://www.yeastgenome.org/locus/ARS1420 ARS1420], [https://www.yeastgenome.org/locus/ARS1421 ARS1421], [https://www.yeastgenome.org/locus/ARS1422 ARS1422], [https://www.yeastgenome.org/locus/ARS1424 ARS1424], [https://www.yeastgenome.org/locus/ARS1426 ARS1426], [https://www.yeastgenome.org/locus/ARS1427 ARS1427] <br>
		+	As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome XIV based on Liachko et al. 2013: ARS1405, ARS1406, ARS1407, ARS1411, ARS1414, ARS1415, ARS1419, ARS1420, ARS1421, ARS1422, ARS1424, ARS1426, ARS1427. <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]
		+	\|-
		+	\| 2013-02-15
		+	\| [https://www.yeastgenome.org/locus/YNL054W-B YNL054W-B]
		+	YNL054W-B was changed from pseudogene to transposable_element_gene. It had been erroneously annotated as a pseudogene based on Kim et al. 1998 which stated that a single nucleotide insertion "would likely render [it] nonfunctional". Lawler et al. 2001 later showed that the insertion was a +1 translational frameshift.<br><br>
		+	'''Kim JM, et al.''' (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8(5):464-78. <br>
		+	[https://www.yeastgenome.org/reference/S000072465 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/9582191 PubMed] \| [https://genome.cshlp.org/content/8/5/464.long Full-Text]<br>
		+	'''Lawler JF Jr, et al.''' (2001) Frameshift signal transplantation and the unambiguous analysis of mutations in the yeast retrotransposon Ty1 Gag-Pol overlap region. J Virol 75(15):6769-75. <br>
		+	[https://www.yeastgenome.org/reference/S000115694 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11435555 PubMed] \| [https://jvi.asm.org/content/75/15/6769.long Full-Text] <br>
		+	\|-
		+	\| 2009-05-06
		+	\| [https://www.yeastgenome.org/locus/ARS1409 ARS1409], [https://www.yeastgenome.org/locus/ARS1410 ARS1410], [https://www.yeastgenome.org/locus/ARS1416 ARS1416], [https://www.yeastgenome.org/locus/ARS1423 ARS1423], [https://www.yeastgenome.org/locus/ARS1425 ARS1425] <br>
		+	The following ARS elements on Chromosome XIV were added to the genome annotation based on Raveendranathan et al. 2006: ARS1409, ARS1410, ARS1416, ARS1423, and ARS1425. <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]<br>