Chromosome IX History

Summary

Chromosome History

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

There have been no sequence changes to Chromosome IX.
The annotation of Chromosome IX has been updated 25 times, affecting 63 features.
Current and past versions can be obtained from SGD's FTP site.

SEQUENCE CHANGES, including any resulting annotation changes

Jump to: Annotation changes

There have been no sequence changes to Chromosome IX

ANNOTATION CHANGES without sequence changes Jump to: Sequence changes

Date Affected Features
2010-01-05 PWR1
New ncRNA PWR1 was added to the genome annotation based on Bumgarner et al. 2009.
Bumgarner SL, et al. (2009) Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106(43):18321-6

2010-01-05 ICR1
New ncRNA ICR1 was added to the genome annotation based on Bumgarner et al. 2009.
Bumgarner SL, et al. (2009) Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106(43):18321-6

2009-05-07 ARS902, ARS904, ARS910, ARS915, ARS918, ARS921
The following ARS elements on Chromosome 9 were added to the genome annotation based on Raveendranathan et al. 2006: ARS902, ARS904, ARS910, ARS915, ARS918, and ARS921.
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

2007-04-04 YIL123W
SIM1/YIL123W mRNA contains an intron in the 5' untranslated region (UTR).
Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7

2007-04-03 YILWdelta2
YILCdelta2, a Ty2 LTR on Chromosome IX, was mistakenly annotated on the wrong strand (i.e., on Crick instead of Watson). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YILWdelta2 and is annotated on the Watson strand. Thanks go to Bertrand Llorente for bringing this annotation error to our attention. The name YILCdelta2 is being retained as an alias.
2006-10-03 ARS923
ARS923, also known as ARS913.5, was added to the genome annotation based on Nieduszynski et al. 2006.
Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9

2006-09-08 ARS909, ARS911, ARS912, ARS914, ARS919, ARS920, ARS922
The following new ARS elements on Chromosome IX were added to SGD based on Nieduszynski et al. 2006: ARS909, ARS911, ARS912, ARS914, ARS919, ARS920, ARS922.
Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9

2006-09-08 ARS913
The coordinates of ARS element ARS901, also known as ARS913, were updated based on Nieduszynski et al. 2006.
Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9

2006-05-09 CEN9
The previously annotated 3' boundary of CEN9 was moved 1 bp upstream to coincide with the 3' end of CDEIII, to more accurately reflect current knowledge regarding centromere structure in Saccharomyces cerevisiae.
Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60

Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68

2006-01-24 YIL053W
Based on 5' SAGE transcription start site data and experimental verification of the start methionine, the start site for YIL053W was moved 63 bp downstream. As a consequence, YIL053W was shorted on the 5' end, altering the N-terminus and shortening the size of the predicted protein from 271 amino acids to 250 amino acids.
Norbeck J and Blomberg A (1997) Metabolic and regulatory changes associated with growth of Saccharomyces cerevisiae in 1.4 M NaCl. Evidence for osmotic induction of glycerol dissimilation via the dihydroxyacetone pathway. J Biol Chem 272(9):5544-54

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

2006-01-23 YIL043C
Based on based on 5' SAGE TSS data, Zhang and Dietrich suggest that the start site for CBR1/YIL043C be moved 114 nt (38 codons) downstream. These data corroborate the start site that Kellis et al. predicted based on the alignment of multiple orthologous sequences. This change has been incorporated into SGD and the numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly.
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54

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

2005-11-22 YIL076W
Based on 5' SAGE transcription start site data and experimental verification of the start methionine, the start site for YIL076W was moved 189 bp downstream. As a consequence, YIL076W was shortened on the 5' end, altering the N-terminus and shortening the size of the predicted protein from 359 amino acids to 296 amino acids.
Duden R, et al. (1998) epsilon-COP is a structural component of coatomer that functions to stabilize alpha-COP. EMBO J 17(4):985-95

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

2005-11-21 YIL102C-A
Based on comparisons of the genome sequences of six Saccharomyces species, Cliften et al. 2003 suggested that this new ORF, YIL102C-A, be added to the S. cerevisiae genome annotation.
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6

2004-10-12 CEN9
Centromeric DNA elements CDEI, CDEII, and CDEIII were annotated based on Wieland et al. 2001 and Espelin et al. 2003.
Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60

Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68

2003-09-27 YIL073C
Based on the alignment of orthologs in related Saccharomyces species, Cliften et al. proposed an intron and new 5' exon for SPO22/YIL073C. The resulting ORF is in the same frame, but has an 89-residue extension at the N-terminus. This change was reviewed and accepted by SGD curators.
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6

2003-09-22 YIL145C
Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for PAN6/YIL145C be moved 108 nt (36 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.
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54

Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6

2003-09-22 YIR014W
The automated comparison of closely related Saccharomyces species suggests that the start site for YIR014W 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.
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54

Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6

2003-09-09 TEL09L, TEL09L-TR, TEL09L-XC, TEL09L-XR, TEL09L-YP, TEL09R, TEL09R-TR, TEL09R-XC, TEL09R-XR
The chromosomal locations for TEL09L-XC, TEL09L-YP, TEL09R-TR, TEL09R-XR, TEL09R-XC, TEL09R, TEL09L-XR, TEL09L-TR, and TEL09L were generously provided by Ed Louis and Dave Barton (University of Leicester, UK).
2003-07-29 YIL002W-A, YIL046W-A, YIR018C-A, YIR021W-A
Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome IX ORFs: YIL002W-A, YIL046W-A, YIR018C-A, and YIR021W-A.
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

Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51

Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20

2003-07-29 YIL020C-A, YIL029W-A, YIL030W-A, YIL047C-A, YIL066W-A, YIL068W-A, YIL071W-A, YIL100C-A, YIL115W-A, YIL142C-A, YIL156W-A, YIL171W-A, YIR017W-A, YIR020C-B, YIR023C-A, YIR030W-A, YIR036W-A
Thanks to MIPS for providing the coordinates of the following Chromosome IX ORFs: YIL020C-A, YIL029W-A, YIL030W-A, YIL047C-A, YIL066W-A, YIL068W-A, YIL071W-A, YIL100C-A, YIL115W-A, YIL142C-A, YIL156W-A, YIL171W-A, YIR017W-A, YIR020C-B, YIR023C-A, YIR030W-A, and YIR036W-A.
2003-07-29 YIL021C-A, YIL105W-A, YIL177W-A
Thanks to Kumar et al. for providing the coordinates of the following Chromosome IX ORFs: YIL021C-A, YIL105W-A, and YIL177W-A.
Kumar A, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63

2003-07-29 YIL134C-A
Thanks to Kessler et al. for providing the coordinates of YIL134C-A.
Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71

2003-07-29 YIL156W-B
Thanks to Brachat et al and Cliften et al. for providing the coordinates of YIL156W-B.
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

Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6

2001-03-06 ARS913
Courtesy of Prof. BiK Tye; based on Ph. D. thesis of Dr. Clarence Chan
1999-11-17 YIL106W
Spingola et al. 1999 identified an intron in YIL106W that was not previously annotated, and also identified a different start codon. The intron has been added, and the start shifted upstream. The old chromosomal coordinates for YIL106W were 166731-167441 (coding 1-711). The new chromosomal coordinates are 166412-167441 (coding 1-20..106-1030).
Spingola M, et al. (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5(2):221-34

Date	Affected Features
2010-01-05	PWR1
	New ncRNA PWR1 was added to the genome annotation based on Bumgarner et al. 2009. *Bumgarner SL, et al.* (2009)** Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106(43):18321-6
2010-01-05	ICR1
	New ncRNA ICR1 was added to the genome annotation based on Bumgarner et al. 2009. *Bumgarner SL, et al.* (2009)** Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106(43):18321-6
2009-05-07	ARS902, ARS904, ARS910, ARS915, ARS918, ARS921
	The following ARS elements on Chromosome 9 were added to the genome annotation based on Raveendranathan et al. 2006: ARS902, ARS904, ARS910, ARS915, ARS918, and ARS921. *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
2007-04-04	YIL123W
	SIM1/YIL123W mRNA contains an intron in the 5' untranslated region (UTR). *Juneau K, et al.* (2007)** High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7
2007-04-03	YILWdelta2
	YILCdelta2, a Ty2 LTR on Chromosome IX, was mistakenly annotated on the wrong strand (i.e., on Crick instead of Watson). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YILWdelta2 and is annotated on the Watson strand. Thanks go to Bertrand Llorente for bringing this annotation error to our attention. The name YILCdelta2 is being retained as an alias.
2006-10-03	ARS923
	ARS923, also known as ARS913.5, was added to the genome annotation based on Nieduszynski et al. 2006. *Nieduszynski CA, et al.* (2006)** Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9
2006-09-08	ARS909, ARS911, ARS912, ARS914, ARS919, ARS920, ARS922
	The following new ARS elements on Chromosome IX were added to SGD based on Nieduszynski et al. 2006: ARS909, ARS911, ARS912, ARS914, ARS919, ARS920, ARS922. *Nieduszynski CA, et al.* (2006)** Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9
2006-09-08	ARS913
	The coordinates of ARS element ARS901, also known as ARS913, were updated based on Nieduszynski et al. 2006. *Nieduszynski CA, et al.* (2006)** Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9
2006-05-09	CEN9
	The previously annotated 3' boundary of CEN9 was moved 1 bp upstream to coincide with the 3' end of CDEIII, to more accurately reflect current knowledge regarding centromere structure in Saccharomyces cerevisiae. *Wieland G, et al.* (2001)** Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60 *Espelin CW, et al.* (2003)** Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68
2006-01-24	YIL053W
	Based on 5' SAGE transcription start site data and experimental verification of the start methionine, the start site for YIL053W was moved 63 bp downstream. As a consequence, YIL053W was shorted on the 5' end, altering the N-terminus and shortening the size of the predicted protein from 271 amino acids to 250 amino acids. Norbeck J and Blomberg A (1997) Metabolic and regulatory changes associated with growth of Saccharomyces cerevisiae in 1.4 M NaCl. Evidence for osmotic induction of glycerol dissimilation via the dihydroxyacetone pathway. J Biol Chem 272(9):5544-54 Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51
2006-01-23	YIL043C
	Based on based on 5' SAGE TSS data, Zhang and Dietrich suggest that the start site for CBR1/YIL043C be moved 114 nt (38 codons) downstream. These data corroborate the start site that Kellis et al. predicted based on the alignment of multiple orthologous sequences. This change has been incorporated into SGD and the numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. *Kellis M, et al.* (2003)** Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51
2005-11-22	YIL076W
	Based on 5' SAGE transcription start site data and experimental verification of the start methionine, the start site for YIL076W was moved 189 bp downstream. As a consequence, YIL076W was shortened on the 5' end, altering the N-terminus and shortening the size of the predicted protein from 359 amino acids to 296 amino acids. *Duden R, et al.* (1998)** epsilon-COP is a structural component of coatomer that functions to stabilize alpha-COP. EMBO J 17(4):985-95 Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51
2005-11-21	YIL102C-A
	Based on comparisons of the genome sequences of six Saccharomyces species, Cliften et al. 2003 suggested that this new ORF, YIL102C-A, be added to the S. cerevisiae genome annotation. *Cliften P, et al.* (2003)** Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
2004-10-12	CEN9
	Centromeric DNA elements CDEI, CDEII, and CDEIII were annotated based on Wieland et al. 2001 and Espelin et al. 2003. *Wieland G, et al.* (2001)** Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60 *Espelin CW, et al.* (2003)** Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68
2003-09-27	YIL073C
	Based on the alignment of orthologs in related Saccharomyces species, Cliften et al. proposed an intron and new 5' exon for SPO22/YIL073C. The resulting ORF is in the same frame, but has an 89-residue extension at the N-terminus. This change was reviewed and accepted by SGD curators. *Cliften P, et al.* (2003)** Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
2003-09-22	YIL145C
	Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for PAN6/YIL145C be moved 108 nt (36 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. *Kellis M, et al.* (2003)** Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 *Cliften P, et al.* (2003)** Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
2003-09-22	YIR014W
	The automated comparison of closely related Saccharomyces species suggests that the start site for YIR014W 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. *Kellis M, et al.* (2003)** Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 *Cliften P, et al.* (2003)** Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
2003-09-09	TEL09L, TEL09L-TR, TEL09L-XC, TEL09L-XR, TEL09L-YP, TEL09R, TEL09R-TR, TEL09R-XC, TEL09R-XR
	The chromosomal locations for TEL09L-XC, TEL09L-YP, TEL09R-TR, TEL09R-XR, TEL09R-XC, TEL09R, TEL09L-XR, TEL09L-TR, and TEL09L were generously provided by Ed Louis and Dave Barton (University of Leicester, UK).
2003-07-29	YIL002W-A, YIL046W-A, YIR018C-A, YIR021W-A
	Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome IX ORFs: YIL002W-A, YIL046W-A, YIR018C-A, and YIR021W-A. *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 *Velculescu VE, et al.* (1997)** Characterization of the yeast transcriptome. Cell 88(2):243-51 *Oshiro G, et al.* (2002)** Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20
2003-07-29	YIL020C-A, YIL029W-A, YIL030W-A, YIL047C-A, YIL066W-A, YIL068W-A, YIL071W-A, YIL100C-A, YIL115W-A, YIL142C-A, YIL156W-A, YIL171W-A, YIR017W-A, YIR020C-B, YIR023C-A, YIR030W-A, YIR036W-A
	Thanks to MIPS for providing the coordinates of the following Chromosome IX ORFs: YIL020C-A, YIL029W-A, YIL030W-A, YIL047C-A, YIL066W-A, YIL068W-A, YIL071W-A, YIL100C-A, YIL115W-A, YIL142C-A, YIL156W-A, YIL171W-A, YIR017W-A, YIR020C-B, YIR023C-A, YIR030W-A, and YIR036W-A.
2003-07-29	YIL021C-A, YIL105W-A, YIL177W-A
	Thanks to Kumar et al. for providing the coordinates of the following Chromosome IX ORFs: YIL021C-A, YIL105W-A, and YIL177W-A. *Kumar A, et al.* (2002)** An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63
2003-07-29	YIL134C-A
	Thanks to Kessler et al. for providing the coordinates of YIL134C-A. *Kessler MM, et al.* (2003)** Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71
2003-07-29	YIL156W-B
	Thanks to Brachat et al and Cliften et al. for providing the coordinates of YIL156W-B. *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 *Cliften P, et al.* (2003)** Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
2001-03-06	ARS913
	Courtesy of Prof. BiK Tye; based on Ph. D. thesis of Dr. Clarence Chan
1999-11-17	YIL106W
	Spingola et al. 1999 identified an intron in YIL106W that was not previously annotated, and also identified a different start codon. The intron has been added, and the start shifted upstream. The old chromosomal coordinates for YIL106W were 166731-167441 (coding 1-711). The new chromosomal coordinates are 166412-167441 (coding 1-20..106-1030). *Spingola M, et al.* (1999)** Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5(2):221-34

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