Chromosome VI History - Revision history

Sage: /* Annotation Changes without sequence changes */

2019-10-04T22:32:08Z

‎Annotation Changes without sequence changes

Sage: /* Annotation Changes without sequence changes */

2019-10-04T22:25:08Z

‎Annotation Changes without sequence changes

Sage at 22:09, 4 October 2019

2019-10-04T22:09:21Z

Sage: /* Sequence Changes */

2019-10-04T21:56:49Z

‎Sequence Changes

Sage: /* Sequence Changes */

2019-10-04T21:52:01Z

‎Sequence Changes

Sage: /* Sequence Changes */

2019-10-04T21:43:56Z

‎Sequence Changes

Show changes

Sage at 19:58, 4 October 2019

2019-10-04T19:58:20Z

Sage: Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome VI systematic reference sequence since its intial release on 1996-07-31.
*The se..."

2019-10-04T19:54:09Z

Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome VI systematic reference sequence since its intial release on 1996-07-31. <br> *The se..."

New page

This page lists all sequence and annotation changes that have been made to the Chromosome VI systematic reference sequence since its intial release on 1996-07-31. <br>
*The sequence of Chromosome VI has been updated '''36''' times, affecting '''43''' features. <br>
*The annotation of Chromosome VI has been updated '''24''' times, affecting '''39''' features. <br>
*Current and past versions can be obtained from SGD's [https://www.yeastgenome.org/downloads Download site].

__FORCETOC__

=Sequence Changes=

{| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
! Date !! Affected Features !! Start Coordinate of Change !! End Coordinate of Change !! Type of Change !! Old Sequence !! New Sequence

← Older revision		Revision as of 22:32, 4 October 2019
Line 703:		Line 703:
	'''Kessler MM, et al.''' (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71. <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>		[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/YFL013W-A YFL013W-A], [https://www.yeastgenome.org/locus/YFL031C-A YFL031C-A], [https://www.yeastgenome.org/locus/YFR032C-B YFR032C-B], [https://www.yeastgenome.org/locus/YFR034W-A YFR034W-A] <br>
		+	Thanks to Kumar et al. for providing the coordinates of the following ORFs on Chromosome VI: YFL013W-A, YFL031C-A, YFR032C-B, YFR034W-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/YFL015W-A YFL015W-A], [https://www.yeastgenome.org/locus/YFL021C-A YFL021C-A], [https://www.yeastgenome.org/locus/YFR036W-A YFR036W-A], [https://www.yeastgenome.org/locus/YFR052C-A YFR052C-A] <br>
		+	Thanks to [https://bioinformatik.wzw.tum.de/index.php?id=63 MIPS] for providing the coordinates of the following ORFs on Chromosome VI: YFL015W-A, YFL021C-A, YFR036W-A, YFR052C-A.<br><br>
		+	\|-
		+	\| 2003-03-13
		+	\| [https://www.yeastgenome.org/locus/YFR024C YFR024C], [https://www.yeastgenome.org/locus/YFR024C-A YFR024C-A] <br>
		+	YFR024C is not a genuine ORF, but is the C-terminus of LSB3/YFR024C-A. The LSB3 gene contains an intron that has been demonstrated to be spliced. The ORF YFR024C has been deleted and the name YFR024C has been made an alias for LSB3/YFR024C-A. <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>
		+	\|-
		+	\| 2003-03-06
		+	\| [https://www.yeastgenome.org/locus/RUF7 RUF7] <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>
		+	\|-
		+	\| 2001-03-15
		+	\| [https://www.yeastgenome.org/locus/ARS603.5 ARS603.5] <br>
		+	Coordinates courtesy of Katsuhiro Shirahige - Personal communication <br><br>
		+	\|-
		+	\| 2001-03-02
		+	\| [https://www.yeastgenome.org/locus/ARS601 ARS601], [https://www.yeastgenome.org/locus/ARS602 ARS602], [https://www.yeastgenome.org/locus/ARS603 ARS603], [https://www.yeastgenome.org/locus/ARS604 ARS604], [https://www.yeastgenome.org/locus/ARS605 ARS605], [https://www.yeastgenome.org/locus/ARS606 ARS606], [https://www.yeastgenome.org/locus/ARS607 ARS607], [https://www.yeastgenome.org/locus/ARS608 ARS608], [https://www.yeastgenome.org/locus/ARS609 ARS609] <br>
		+	The coordinates for the following ARS elements on Chromosome VI are courtesy of Katsuhiro Shirahige, based on Shirahige et al. 1993: ARS601, ARS602, ARS603, ARS604, ARS605, ARS606, ARS607, ARS608, ARS609.<br><br>
		+	'''Shirahige K, et al.''' (1993) Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol Cell Biol 13(8):5043-56. <br>
		+	[https://www.yeastgenome.org/reference/S000050050 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/8336734 PubMed] \| [https://mcb.asm.org/content/13/8/5043.long Full-Text] <br>
		+
		+	\|}

← Older revision		Revision as of 22:25, 4 October 2019
Line 623:		Line 623:
	'''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>		'''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>		[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>
		+	\|-
		+	\| 2007-03-08
		+	\| [https://www.yeastgenome.org/locus/ARS601 ARS601], [https://www.yeastgenome.org/locus/ARS602 ARS602], [https://www.yeastgenome.org/locus/ARS604 ARS604], [https://www.yeastgenome.org/locus/ARS605 ARS605], [https://www.yeastgenome.org/locus/ARS606 ARS606], [https://www.yeastgenome.org/locus/ARS607 ARS607], [https://www.yeastgenome.org/locus/ARS608 ARS608], [https://www.yeastgenome.org/locus/ARS609 ARS609] <br>
		+	ACS annotated based on Xu et al. 2006 and Shirahige et al. 1993. <br> <br>
		+	'''Shirahige K, et al.''' (1993) Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol Cell Biol 13(8):5043-56. <br>
		+	[https://www.yeastgenome.org/reference/S000050050 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/8336734 PubMed] \| [https://mcb.asm.org/content/13/8/5043.long Full-Text] <br>
		+	'''Xu W, et al.''' (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7():276. <br>
		+	[https://www.yeastgenome.org/reference/S000119399 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17067396 PubMed] \| [https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-276 Full-Text] <br>
		+	\|-
		+	\| 2007-03-08
		+	\| [https://www.yeastgenome.org/locus/ARS603.5 ARS603.5] <br>
		+	ACS was annotated based on Xu et al. 2006 and Yamashita et al. 1997. <br><br>
		+	'''Xu W, et al.''' (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7():276. <br>
		+	[https://www.yeastgenome.org/reference/S000119399 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17067396 PubMed] \| [https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-276 Full-Text] <br>
		+	'''Yamashita M, et al.''' (1997) The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI. Genes Cells 2(11):655-65. <br>
		+	[https://www.yeastgenome.org/reference/S000121132 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/9491800 PubMed] \| [https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-2443.1997.1530351.x?sid=nlm%3Apubmed Full-Text] <br>
		+	\|-
		+	\| 2007-03-08
		+	\| [https://www.yeastgenome.org/locus/ARS603 ARS603] <br>
		+	Both ACS's within ARS603 were annotated based on Xu et al. 2006 and Shirahige et al. 1993.<br><br>
		+	'''Shirahige K, et al.''' (1993) Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol Cell Biol 13(8):5043-56. <br>
		+	[https://www.yeastgenome.org/reference/S000050050 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/8336734 PubMed] \| [https://mcb.asm.org/content/13/8/5043.long Full-Text] <br>
		+	'''Xu W, et al.''' (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7():276. <br>
		+	[https://www.yeastgenome.org/reference/S000119399 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17067396 PubMed] \| [https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-276 Full-Text] <br>
		+	\|-
		+	\| 2007-03-08
		+	\| [https://www.yeastgenome.org/locus/ARS610 ARS610] <br>
		+	ARS610 was added to the genome annotation based on Xu et al. 2006. <br><br>
		+	'''Xu W, et al.''' (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics 7():276. <br>
		+	[https://www.yeastgenome.org/reference/S000119399 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/17067396 PubMed] \| [https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-276 Full-Text] <br>
		+	\|-
		+	\| 2006-05-08
		+	\| [https://www.yeastgenome.org/locus/CEN6 CEN6] <br>
		+	The previously annotated 5' boundary of CEN6 was slightly adjusted to coincide with the 5' end of CDEI, 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>
		+	\|-
		+	\| 2006-03-02
		+	\| [https://www.yeastgenome.org/locus/ARS600 ARS600] <br>
		+	This ARS element ARS600 (originally published as ARS120) was added to the genome annotation based on Eisenberg et al. 1988 and Wyrick et al. 2001. ARS120 was originally added to SGD as "not in systematic sequence of S288C". <br><br>
		+	'''Eisenberg S, et al.''' (1988) Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences. Proc Natl Acad Sci U S A 85(3):743-6. <br>
		+	[https://www.yeastgenome.org/reference/S000049674 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/3277180 PubMed] \| [https://www.pnas.org/content/85/3/743 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>
		+	\|-
		+	\| 2004-10-12
		+	\| [https://www.yeastgenome.org/locus/CEN6 CEN6] <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>
		+	\|-
		+	\| 2004-04-01
		+	\| [https://www.yeastgenome.org/locus/RUF7 RUF7] <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>
		+	\|-
		+	\| 2003-09-09
		+	\| [https://www.yeastgenome.org/locus/TEL06L TEL06L], [https://www.yeastgenome.org/locus/TEL06R TEL06R] <br>
		+	The chromosomal locations for the following telomeric features on Chromosome VI were generously provided by Ed Louis and Dave Barton (University of Leicester, UK): TEL06L, TEL06L-XC, TEL06L-XR, TEL06L-TR, TEL06L-YP, TEL06R, TEL06R-XC, TEL06R-TR.<br><br>
		+	\|-
		+	\| 2003-07-29
		+	\| [https://www.yeastgenome.org/locus/YFR009W-A YFR009W-A], [https://www.yeastgenome.org/locus/YFR010W-A YFR010W-A] <br>
		+	Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following ORFs on Chromosome VI: YFR009W-A, YFR010W-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/YFL041W-A YFL041W-A] <br>
		+	Thanks to Kessler et al. for providing the coordinates of ORF YFL041W-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>

← Older revision		Revision as of 22:09, 4 October 2019
Line 536:		Line 536:
	'''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>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2001-05-29
		+	\| [https://www.yeastgenome.org/locus/YFL042C YFL042C], [https://www.yeastgenome.org/locus/YFL043C YFL043C] <br>
		+	\| 46151
		+	\| 46151
		+	\| Deletion
		+	\| C
		+	\|
		+	\|-
		+	\| \|\| colspan="6" \| Due to the deletion of G at chromosomal coordinate 46151, which was within the ORF YFL043C, YFL043C is now part of YFL042C. The new coordinates for YFL042C are 47744-45720. See Genbank file YSCCHRVIN. ''The old coordinates for YFL042C were 47745-46078, and for YFL043C were 46157-45720.''
		+	<pre>Old: 46141 CACGTTATTTCCGTCATTCCAACGGATTAGATACCTTGTCTTAGTTGAGAAACTACCACC 46200
		+	\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 46141 CACGTTATTTC-GTCATTCCAACGGATTAGATACCTTGTCTTAGTTGAGAAACTACCACC 46199</pre>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2001-05-29
		+	\| [https://www.yeastgenome.org/locus/YFL031W YFL031W] <br>
		+	\| 75751
		+	\| 75751
		+	\| Insertion
		+	\|
		+	\| C
		+	\|-
		+	\| \|\| colspan="6" \| A single C was inserted after the C at chromosomal coordinate 75751 (see GenBank file YSCCHRVIN). In addition, a new intron was annotated at relative coordinates 662-913. As a result, the chromosomal coordinates for ORF YFL031W are now 75177-75837..76090-76145, with relative coordinates 1-661..914-969. ''The old chromosomal coordinates for YFL031W were 75178-75780, with old relative coordinates 1-603.''
		+	<pre>Old: 75721 AACAACAATTTGTTTGATGCGGTGGCCTCGC-GTTGGCAGACCCACTCTGCGACGATATA 75779
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 75720 AACAACAATTTGTTTGATGCGGTGGCCTCGCCGTTGGCAGACCCACTCTGCGACGATATA 75779</pre>
		+
		+	\|}
		+
		+	<br><br>
		+
		+	=Annotation Changes ''without sequence changes''=
		+	{\| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
		+	! Date !! Affected Features
		+	\|-
		+	\| 2014-11-18
		+	\| [https://www.yeastgenome.org/locus/ARS600 ARS600], [https://www.yeastgenome.org/locus/ARS603 ARS603], [https://www.yeastgenome.org/locus/ARS606 ARS606] <br>
		+	The chromosomal coordinates of the following ARS elements on Chromosome VI were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS600, ARS603, ARS606. <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/ARS600.4 ARS600.4], [https://www.yeastgenome.org/locus/ARS603.1 ARS603.1] <br>
		+	The following new ARS elements on Chromosome VI were added to the genome annotation based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS600.4, ARS603.1.<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/YFL056C YFL056C], [https://www.yeastgenome.org/locus/YFL057C YFL057C] <br>
		+	The ORF AAD16/YFL057C was merged into neighboring ORF AAD6/YFL056C and the combined feature is now annotated as a pseudogene. This update was made as part of SGD's genome annotation revision R64.2.<br> <br>
		+	'''Delneri D, et al.''' (1999) Analysis of the seven-member AAD gene set demonstrates that genetic redundancy in yeast may be more apparent than real. Genetics 153(4):1591-600. <br>
		+	[https://www.yeastgenome.org/reference/S000043843 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10581269 PubMed] \| [https://www.genetics.org/content/153/4/1591.long Full-Text] <br>
		+	\|-
		+	\| 2009-05-04
		+	\| [https://www.yeastgenome.org/locus/RUF20 RUF20], [https://www.yeastgenome.org/locus/RUF21 RUF21], [https://www.yeastgenome.org/locus/RUF22 RUF22], [https://www.yeastgenome.org/locus/RUF23 RUF23] <br>
		+	The following RNA features were added to the S. cerevisiae genome annotation based on Kavanaugh & Dietrich 2009: RUF20, RUF21, RUF22, and RUF23. ''Note that Kavanaugh & Dietrich state that the 3' ends of RUF22 and RUF23 are uncertain, meaning that these two RNAs may possibly be longer than currently annotated.''<br> <br>
		+	'''Kavanaugh LA and Dietrick FS''' (2009) Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae. PLoS Genet 5(1):e1000321. <br>
		+	[https://www.yeastgenome.org/reference/S000128754 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/19119416 PubMed] \| [https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000321 Full-Text] <br>
		+	\|-
		+	\| 2008-06-02
		+	\| [https://www.yeastgenome.org/locus/YFR024C-A YFR024C-A] <br>
		+	Based on the sequencing of the cloned cDNA, as the genomic DNA has an intron, Kathryn Ayscough and E.G. Allwood from the University of Sheffield conclude that the intron is not spliced at the predicted site, but rather 24 nt upstream. This annotation was updated in SGD, and as a result, the predicted protein product is 8 amino acids longer. The relative coding coordinates had been 1-47..166-1474, but are now 1-47..142-1474. Special thanks to Kathryn Ayscough and E.G. Allwood from the University of Sheffield for bringing this error to our attention. <br><br>
		+
		+	This annotation change is also supported by RNA sequencing data from Yassour et al. 2009.<br><br>
		+	'''Ayscough K and Allowed E''' (2008) <br>
		+	[https://www.yeastgenome.org/reference/S000126577 SGD paper] <br>
		+	'''Yassour M, et al.''' (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106(9):3264-9. <br>
		+	[https://www.yeastgenome.org/reference/S000129301 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/19208812 PubMed] \| [https://www.pnas.org/content/106/9/3264 Full-Text] <br>
		+	\|-
		+	\| 2007-04-04
		+	\| [https://www.yeastgenome.org/locus/YFR032C-A YFR032C-A] <br>
		+	RPL29/YFR032C-A 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>
		+	\|-
		+	\| 2007-04-04
		+	\| [https://www.yeastgenome.org/locus/YFR045W YFR045W] <br>
		+	Based on cDNA data from Miura et al. and sequence conservation among closely related fungal species, a new intron and 5' exon were added to YFR045W. This alters and extends the N-terminus, changing the size of the protein product from 285 to 309 amino acids. Special thanks to Michel Satre for bringing this update to our attention. <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>

← Older revision		Revision as of 21:56, 4 October 2019
Line 508:		Line 508:
	'''Robben J, et al.''' (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702. <br>		'''Robben J, et al.''' (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702. <br>
	[https://www.yeastgenome.org/reference/S000070321 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12185839 PubMed] \| [https://onlinelibrary.wiley.com/doi/full/10.1002/yea.870 Full-Text] <br>		[https://www.yeastgenome.org/reference/S000070321 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12185839 PubMed] \| [https://onlinelibrary.wiley.com/doi/full/10.1002/yea.870 Full-Text] <br>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2003-09-26
		+	\| [https://www.yeastgenome.org/locus/YFR040W YFR040W] <br>
		+	\| 234451
		+	\| 234451
		+	\| Deletion
		+	\| G
		+	\|
		+	\|-
		+	\| \|\| colspan="6" \| Due to the deletion of a G at 234450 on Chr VI, the coordinates of ORF YFR040W changed from 234521-237238 to 234229-237237. <br>
		+	References:<br>
		+
		+	1. ''Sequence verification in AB972 (S288c derivative strain) background by SGD''.<br>
		+	2. ''Personal communication from Margaret Shirra, University of Pittsburgh''.<br>
		+	<pre>Old: 234421 CATGGTGATGAAGTGAAAACGGCACGTGGGAGATCAGAAGAGTCGATTTGAGAAGGATGA 234480
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 234421 CATGGTGATGAAGTGAAAACGGCACGTGG-AGATCAGAAGAGTCGATTTGAGAAGGATGA 234479</pre>
		+	'''Luke MM, et al.''' (1996) The SAP, a new family of proteins, associate and function positively with the SIT4 phosphatase. Mol Cell Biol 16(6):2744-55. <br>
		+	[https://www.yeastgenome.org/reference/S000055325 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/8649382 PubMed] \| [https://mcb.asm.org/content/16/6/2744.long Full-Text] <br>
		+	'''Jablonowski D, et al.''' (2001) Sit4p protein phosphatase is required for sensitivity of Saccharomyces cerevisiae to Kluyveromyces lactis zymocin. Genetics 159(4):1479-89. <br>
		+	[https://www.yeastgenome.org/reference/S000068918 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/11779790 PubMed] \| [https://www.genetics.org/content/159/4/1479.long Full-Text] <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>
		+	'''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>

← Older revision		Revision as of 21:52, 4 October 2019
Line 420:		Line 420:
	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>		'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]		[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2004-02-05
		+	\| [https://www.yeastgenome.org/locus/YFR038W YFR038W] <br>
		+	\| 231670
		+	\| 231670
		+	\| Deletion
		+	\| G
		+	\|
		+	\|-
		+	\| \|\| colspan="6" \| Based on the automated comparison of related fungi, Kellis et al. and Brachat et al. suggested that the stop site for YFR038W be moved 226 nt downstream. Hui-fen Kuo and Eric Richards resequenced this portion of the genome and found that a G nt. should be deleted (personal communication to SGD). This sequence error was confirmed by SGD. As a consequence of this sequence change, YFR038W was extended 226 nt at the 3' end, altering the the C-terminus and increasing the size of the predicted protein from 778 to 853 amino acids.
		+	<pre>New: 231648 AAAAATTGGCGTTAAATGAAGG-TTCTTTTTTGAAGGCAAA 231687
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old: 231648 AAAAATTGGCGTTAAATGAAGGGTTCTTTTTTGAAGGCAAA 231688</pre>
		+	'''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>
		+	'''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>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2004-02-05
		+	\| [https://www.yeastgenome.org/locus/YFR045W YFR045W] <br>
		+	\| 242181
		+	\| 242181
		+	\| Insertion
		+	\|
		+	\| G
		+	\|-
		+	\| \|\| colspan="6" \| Based on the automated comparison of related ''Saccharomyces'' species, Kellis et al. and Brachat et al. suggested that the start site for YFR045W be moved 320 nt upstream. Belenkiy R et al. demonstrated a G nt insertion in that region and this sequence change was confirmed in S288c, by SGD. As a consequence of this sequence change, YFR045W was extended 320 nt at the 5' end, altering the the N-terminus and increasing the size of the predicted protein from 537 to 858 amino acids. Note that Belenkiy et al. also demonstrated a silent G to C substitution 701 nts downstream from the new start site; however, SGD could not confirm this sequence change in S288c, so it has not been incorporated.
		+	<pre>New: 242152 TAAAGACTGGTTTACAATTGCAACCGAAGGGTACCGCTTTCGAAATCATTTTACCTCAGA 242211
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old: 242152 TAAAGACTGGTTTACAATTGCAACCGAAGG-TACCGCTTTCGAAATCATTTTACCTCAGA 242210</pre>
		+	'''Belenkiy R, et al.''' (2000) The yeast mitochondrial transport proteins: new sequences and consensus residues, lack of direct relation between consensus residues and transmembrane helices, expression patterns of the transport protein genes, and protein-protein interactions with other proteins. Biochim Biophys Acta 1467(1):207-18. <br>
		+	[https://www.yeastgenome.org/reference/S000049213 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/10930523 PubMed] \| [https://www.sciencedirect.com/science/article/pii/S0005273600002224?via%3Dihub Full-Text] <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>
		+	'''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>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2003-09-26
		+	\| [https://www.yeastgenome.org/locus/YFR050C YFR050C], [https://www.yeastgenome.org/locus/YFR051C YFR051C] <br>
		+	\| 250082
		+	\| 250082
		+	\| Deletion
		+	\| G
		+	\|
		+	\|-
		+	\| \|\| colspan="6" \| A single G nucleotide was deleted from the intergenic region between ORFs YFR050C and YFR051C.
		+	<pre>Old: 250051 TAAACTATATATATAGAAGGACGAAAGAAAAGGATACCTCGATTTTTATTTATTTAGTTT 250110
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 250051 TAAACTATATATATAGAAGGACGAAAGAAAAG-ATACCTCGATTTTTATTTATTTAGTTT 250109</pre>
		+	'''Robben J, et al.''' (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702. <br>
		+	[https://www.yeastgenome.org/reference/S000070321 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12185839 PubMed] \| [https://onlinelibrary.wiley.com/doi/full/10.1002/yea.870 Full-Text] <br>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2003-09-26
		+	\| [https://www.yeastgenome.org/locus/YFL006W YFL006W], [https://www.yeastgenome.org/locus/YFL007W YFL007W] <br>
		+	\| 128870
		+	\| 128870
		+	\| Insertion
		+	\|
		+	\| G
		+	\|-
		+	\| \|\| colspan="6" \| Due to the insertion of a G at 128870 on Chromosome VI, YFL006W has been merged with BLM10/YFL007W. YFL006W is now an alias of BLM10/YFL007W. ''Personal communication from Tim Formosa, University of Utah''.
		+	<pre>Old: 128841 TTTGATCACCCATACGATCAGGTTCGCCAG-CTGTCGCTAAACTATTGACGACCTTAGTT 128899
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 128841 TTTGATCACCCATACGATCAGGTTCGCCAGGCTGTCGCTAAACTATTGACGACCTTAGTT 128900</pre>
		+	'''Robben J, et al.''' (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702. <br>
		+	[https://www.yeastgenome.org/reference/S000070321 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12185839 PubMed] \| [https://onlinelibrary.wiley.com/doi/full/10.1002/yea.870 Full-Text] <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>
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2003-09-26
		+	\| [https://www.yeastgenome.org/locus/TEL06R TEL06R], [https://www.yeastgenome.org/locus/TEL06R-XC TEL06R-XC] <br>
		+	\| 270023
		+	\| 270023
		+	\| Insertion
		+	\|
		+	\| G
		+	\|-
		+	\| \|\| colspan="6" \| After sequence verification in AB972 (S288c derivative) by SGD, a single G nucleotide was inserted after chromosomal coordinate 270023. This change lies within TEL06R-XC, the X element core sequence of TEL06R, the right telomere of chromosome VI.
		+	<pre>Old: 270000 TACTATTGATGGAAATGAGGACTG-GTCATGGGGCGCAATGGAGTGAAGTAATATATACT 270058
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	New: 270000 TACTATTGATGGAAATGAGGACTGGGTCATGGGGCGCAATGGAGTGAAGTAATATATACT 270059</pre>
		+	'''Robben J, et al.''' (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702. <br>
		+	[https://www.yeastgenome.org/reference/S000070321 SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/12185839 PubMed] \| [https://onlinelibrary.wiley.com/doi/full/10.1002/yea.870 Full-Text] <br>

← Older revision		Revision as of 19:58, 4 October 2019
Line 10:		Line 10:
	{\| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"		{\| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
	! Date !! Affected Features !! Start Coordinate of Change !! End Coordinate of Change !! Type of Change !! Old Sequence !! New Sequence		! Date !! Affected Features !! Start Coordinate of Change !! End Coordinate of Change !! Type of Change !! Old Sequence !! New Sequence
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFL034W YFL034W]
		+	\| 66443
		+	\| 66443
		+	\| Substitution
		+	\| C
		+	\| A
		+	\|-
		+	\| \|\| colspan="6" \| Nucleotide change(s) in the coding region of YFL034W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 323 is now Lysine rather than Asparagine.
		+	<pre>New 66421 TATTGACATTAAATCCCACAAGAAACTAGCACATAGATTACAGTTTACCCAGAAGGATAT 66480
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 66419 TATTGACATTAAATCCCACAAGAACCTAGCACATAGATTACAGTTTACCCAGAAGGATAT 66478</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFR040W YFR040W]
		+	\| 236216
		+	\| 236216
		+	\| Substitution
		+	\| C
		+	\| A
		+	\|-
		+	\| \|\| colspan="6" \| Nucleotide change(s) in the coding region of SAP155/YFR040W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 663 is now Asparagine rather than Threonine.
		+	<pre>New 236219 ATGAAGCAAAACATAAAACTTAGGACCGACCCCACGGTCGGGGACCTATTCAAAATCAAA 236278
		+	\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 236206 ATGAAGCAAACCATAAAACTTAGGACCGACCCCACGGTCGGGGACCTATTCAAAATCAAA 236265</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFR019W YFR019W]
		+	\| 191312
		+	\| 191312
		+	\| Substitution
		+	\| T
		+	\| A
		+	\|-
		+	\| \|\| colspan="6" \| Nucleotide change(s) in the coding region of FAB1/YFR019W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 2275 is now Arginine rather than Tryptophan.
		+	<pre>New 191280 AAGCAATGGAGAGGTATATTTTGATGGTTCCTGATCCGTGGTATAGGGAAGGAAATTAAT 191339
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 191268 AAGCAATGGAGAGGTATATTTTGATGGTTCCTGATCCGTGGTATTGGGAAGGAAATTAAT 191327</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFL026W YFL026W]
		+	\| 83382
		+	\| 83382
		+	\| Substitution
		+	\| G
		+	\| A
		+	\|-
		+	\| \|\| colspan="6" \| Nucleotide change(s) in the coding region of STE2/YFL026W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 269 is now Lysine rather than Glutamic Acid.
		+	<pre>New 83341 TTTGTTGGTTCCATCGATAATATTCATCCTCGCATACAGTTTGAAACCAAACCAGGGAAC 83400
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 83339 TTTGTTGGTTCCATCGATAATATTCATCCTCGCATACAGTTTGGAACCAAACCAGGGAAC 83398</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFR020W YFR020W], [https://www.yeastgenome.org/locus/YFRCdelta9 YFRCdelta9] <br>
		+	\| 192393
		+	\| 192393
		+	\| Deletion
		+	\| C
		+	\|
		+	\|-
		+	\| \|\| colspan="6" \| A single nucleotide deletion was made in the intergenic region between Ty1 LTR YFRCdelta9 and ORF YFR020W.
		+	<pre>New 192360 TTTTAGGAATACTGTTGTTCAAGATAGAGCATTTGCATACCTTAT-CGAGGTTCACTATC 192418
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 192348 TTTTAGGAATACTGTTGTTCAAGATAGAGCATTTGCATACCTTATCCGAGGTTCACTATC 192407</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]
		+
		+	\|- style="height:30px; width:30px; text-align:center;"
		+	\| 2011-02-03
		+	\| [https://www.yeastgenome.org/locus/YFR020W YFR020W], [https://www.yeastgenome.org/locus/YFRCdelta9 YFRCdelta9] <br>
		+	\| 192393
		+	\| 192393
		+	\| Insertion
		+	\|
		+	\| T
		+	\|-
		+	\| \|\| colspan="6" \| A single nucleotide insertion was made in the intergenic region between ORFs YFR020W and ATG18/YFR021W.
		+	<pre>New 194759 GTTAGTAATAGTGTTCCAGTTAACTCTGTATCCTTTTCTTCTTCGGCCTGACAATGTCTG 194818
		+	\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|
		+	Old 194748 GTTAGTAATAGTGTTCCAGTTAACTCTGTATCCTTTTC-TCTTCGGCCTGACAATGTCTG 194806</pre>
		+	'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
		+	[http://www.yeastgenome.org/reference/24374639/overview SGD paper] \| [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] \| [http://g3journal.org/content/4/3/389 Full-Text]

Chromosome VI History - Revision history

Sage: /* Annotation Changes without sequence changes */

Sage: /* Annotation Changes without sequence changes */

Sage at 22:09, 4 October 2019

Sage: /* Sequence Changes */

Sage: /* Sequence Changes */

Sage: /* Sequence Changes */

Sage at 19:58, 4 October 2019

Sage: Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome VI systematic reference sequence since its intial release on 1996-07-31. *The se..."

Sage: Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome VI systematic reference sequence since its intial release on 1996-07-31.
*The se..."