Chromosome XVI History

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

• The sequence of Chromosome XVI has been updated 23 times, affecting 16 features.
  
• The annotation of Chromosome XVI has been updated 39 times, affecting 72 features.
  
• Current and past versions can be obtained from SGD's Download site.

Sequence Changes

Date	Affected Features	Start Coordinate of Change	End Coordinate of Change	Type of Change	Old Sequence	New Sequence
2011-02-03	YPL224C	128039	128039	Substitution	T	G
		126768	126768	Insertion		C
	Two nucleotide changes were made within the ORF MMT2/YPL224C, altering its coding sequence: one single nucleotide substitution near the 5' end, and one single nucleotide insertion near the 3' end. The start and majority of the reading frame remain the same, but the C-terminus has changed, and the annotated protein is now 35 amino acids longer. New 126721 ACCTTTAGAGTCAGAGGTTACATCAACAAACTCGACGTCCACCTTCCCCACGTTTGGCAC 126780 |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| Old 126721 ACCTTTAGAGTCAGAGGTTACATCAACAAACTCGACGTCCACCTTCCC-ACGTTTGGCAC 126779 New 127981 CAGGCTTGATGTTCTTATGGCCCTCCCGGCAGCATGGTAACTAGTGTTGTTATAACCTGGCACAAAGGAA 128050 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| Old 127980 CAGGCTTGATGTTCTTATGGCCCTCCCGGCAGCATGGTAACTAGTGTTGTTATAACCTGTCACAAAGGAA 128049 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR035W	642955	642955	Substitution	G	A
		642995	642995	Substitution	C	T
	Nucleotide change(s) in the coding region of GLN1/YPR035W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 251 is now Threonine rather than Alanine, and residue 264 is now Methionine rather than Threonine. New 642949 GGTTGTCACACTAACGTTTCCACCAAGGAAATGAGACAACCAGGTGGTATGAAATACATCGAACAAGCCA 643018 ||||||||| ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| Old 642946 GGTTGTCACGCTAACGTTTCCACCAAGGAAATGAGACAACCAGGTGGTACGAAATACATCGAACAAGCCA 643015 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR097W	727933	727933	Substitution	G	A
	A single nucleotide substitution within the coding region of YPR097W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 848 is now Serine rather than Glycine. New 727918 ATTTTGAGAAGTTCATGAGTGATTTGATCAGGCTTGTTGATGATGTTATCAATGGTCAGT 727977 ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| Old 727916 ATTTTGAGAAGTTCATGGGTGATTTGATCAGGCTTGTTGATGATGTTATCAATGGTCAGT 727975 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR121W	778863	778863	Substitution	T	A
	A single nucleotide substitution within the coding region of THI22/YPR121W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 95 is now Glutamine rather than Histidine. New 778858 CGGCGCTCAAAATATACCAAAGAAAATGGTATCTCAAATATTAGACGCCAATTTACAGGA 778917 ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| Old 778854 CGGCGCTCATAATATACCAAAGAAAATGGTATCTCAAATATTAGACGCCAATTTACAGGA 778913 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPL108W, YPL109C	347528	347528	Insertion		G
		347759	347759	Insertion		C
	Two separate single nucleotides were inserted in the intergenic region between ORFs YPL109C and YPL108W. New 347521 GGTATTATTGCCCCTCATATATTCGGGGTTATTTATTTTTCGTTGCTTGAAGTAAAGCCT 347580 ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| Old 347520 GGTATTATT-CCCCTCATATATTCGGGGTTATTTATTTTTCGTTGCTTGAAGTAAAGCCT 347578 New 347751 CCCTTTCGCGGCACTTTTTCTCTTAGCTCTGCTTGATACATCGACTGGGAACTTCTTCTCTTTGAGCCAA 347820 ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Old 347749 CCCTTTCGCGG-ACTTTTTCTCTTAGCTCTGCTTGATACATCGACTGGGAACTTCTTCTCTTTGAGCCAA 347817 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR121W, YPRWdelta16	778376	778376	Insertion		C
		778302	778302	Insertion		G
	Two single nucleotide insertions were made in the intergenic region between YPRWdelta16 and YPR121W/THI22. New 778258 TTAATGGAATAACGTGATTTTTGTACCAAATTGCCTATTTCAGATTCGGCGTGCGCTTCC 778317 ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| Old 778256 TTAATGGAATAACGTGATTTTTGTACCAAATTGCCTATTTCAGATTC-GCGTGCGCTTCC 778314 New 778368 TGCACGGAAGATCCTTGCAGGAATCAAATACTGCCTTTCACTTTGCAACCTCTTAATCACATAGTAGCAC 778437 |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Old 778365 TGCACGGAAGAT-CTTGCAGGAATCAAATACTGCCTTTCACTTTGCAACCTCTTAATCACATAGTAGCAC 778433 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR035W, YPR036W	643579	643579	Substitution	T	C
	A single nucleotide substitution was made in the intergenic region between ORFs YPR035W/GLN1 and YPR036W/VMA13. New 643559 TCGAATTTTTTCTTTTTTTTTTTCTGCAAAGCGACGCTGTGTTGTATATTGCTCTAAAAT 643618 ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| Old 643556 TCGAATTTTTTCTTTTTTTTTTTTTGCAAAGCGACGCTGTGTTGTATATTGCTCTAAAAT 643615 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPL016W	523639	523639	Substitution	C	T
	A single nucleotide substitution was made within the ORF SWI1/YPL016W. Note that the protein sequence was not changed. New 523619 GATTCCTCCCTAACCAATTTCCTTTGAAAATTCACAGAACTCCTTATTTGACTTCTTTGA 523678 ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| Old 523616 GATTCCTCCCTAACCAATTTCCTCTGAAAATTCACAGAACTCCTTATTTGACTTCTTTGA 523675 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPL016W, YPL017C	520375	520375	Insertion		C
		520378	520378	Substitution	C	G
		520646	520646	Insertion		C
		520818	520818	Deletion	T
	Four single nucleotide changes were made in the intergenic region between ORFs YPL016W/SWI1 and YPL017C/IRC15: two insertions, one substitution, and one deletion. New 520320 AGATGCATGCCTGCAGGTCTGGGTGTACCCCCTGCCTGAGTGTTCCACCCAGGCCTCGCCGGAGGAAAAT 520389 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| Old 520318 AGATGCATGCCTGCAGGTCTGGGTGTACCCCCTGCCTGAGTGTTCCACCCAGGCCTCG-CGCAGGAAAAT 520386 New 520620 CATATTCACATTGCGTTTTAGTCATAACCACCTTCCGGTATTCATCATTCGTATTGAATA 520679 |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| Old 520617 CATATTCACATTGCGTTTTAGTCATAACCA-CTTCCGGTATTCATCATTCGTATTGAATA 520675 New 520800 ATCTCTGCTTTGGCATTTCGCG-TTGTTTCCTCTCACGGATTGCAGATTATTGTTCACCA 520858 |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| Old 520796 ATCTCTGCTTTGGCATTTCGCGTTTGTTTCCTCTCACGGATTGCAGATTATTGTTCACCA 520855 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPL036W, YPL037C	482773	482773	Deletion	T
	A single nucleotide was deleted from the intergenic region between ORFs YPL037C/EGD1 and YPL036W/PMA2. New 482761 AAACATACCCATAAC-TTTTTTTTTTTCATTTTTCGTTGCTGTGTGCTAGTACAATTTAA 482819 ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| Old 482758 AAACATACCCATAACTTTTTTTTTTTTCATTTTTCGTTGCTGTGTGCTAGTACAATTTAA 482817 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2011-02-03	YPR078C, YPR079W	698524	698524	Deletion	A
	A single nucleotide deletion was made in the intergenic region between ORFs YPR078C and YPR079W/MRL1. New 698519 TTCTTCTG-AAAAAAAAAAAAAAAAATTCAAAAAAAGACACCTTTCTACCTTGGCAGTAA 698577 |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| Old 698516 TTCTTCTGAAAAAAAAAAAAAAAAAATTCAAAAAAAGACACCTTTCTACCTTGGCAGTAA 698575 Engel SR, et al. (2014) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. SGD paper | PubMed | Full-Text
2004-07-21	YPL109C	347273	347273	Insertion		T
		347265	347265	Deletion	T
		347285	347285	Insertion		A
		347375	347375	Insertion		T
	The works of Kellis et al. 2003 and Cliften et al. 2003 predicted multiple insertions and deletions in YPL109C, and the sequence errors were confirmed in S288C by SGD. As a consequence of these changes, YPL109C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 590 to 657 amino acids. New: TGTTTTGGAAACGAATTTT-GTGTCAAATAAAAAGCAATTGACGTAGGTATTATGAACTG ||||||||||||||||||| |||||||| |||||||||||| |||||||||||||||||| Old: 347246 TGTTTTGGAAACGAATTTTTGTGTCAAA-AAAAAGCAATTG-CGTAGGTATTATGAACTG 347303 Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-29	YPR089W, YPR090W	713683	713683	Deletion	T
	Due to deletion of a T at position 713683, YPR089W and YPR090W were merged. After merging YPR089W (713271 - 713738 (1-468)) and YPR090W (713728 - 715938 (1-2211)), the coordinates of the merged ORF, YPR089W, are 713271 - 715937 (1-2667). YPR090W is now an alias of YPR089W. Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement

Annotation Changes without sequence changes

Date	Affected Features
2014-11-19	ARS1605, ARS1607, ARS1621, ARS1622, ARS1625 The chromosomal coordinates of the following ARS elements on Chromosome XVI were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS1605, ARS1607, ARS1621, ARS1622, ARS1625. Liachko I, et al. (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. SGD paper | PubMed | Full-Text
2014-11-19	ARS1604, ARS1607, ARS1614, ARS1618, ARS1619, ARS1621, ARS1622, ARS1623, ARS1624, ARS1625, ARS1626, ARS1627, ARS1628, ARS1630, ARS1631 As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome XVI based on Liachko et al. 2013: ARS1604, ARS1607, ARS1614, ARS1618, ARS1619, ARS1621, ARS1622, ARS1623, ARS1624, ARS1625, ARS1626, ARS1627, ARS1628, ARS1630, ARS1631. Liachko I, et al. (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. SGD paper | PubMed | Full-Text
2014-11-19	YPL060C-A YPL060C-A had been erroneously identified as a pseudogene because it was incompletely annotated. As part of SGD's genome annotation revision R64.2, the feature_type of YPL060C-A was changed from pseudogene to transposable_element_gene, and the missing plus_1_translational_frameshift and remainder of the gene were added. Old coordinates: 442742..439428 CDS New coordinates: 442742..439429 CDS 439428..439428 plus_1_translational_frameshift 439427..437333 CDS 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. SGD paper | PubMed | Full-Text 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. SGD paper | PubMed | Full-Text
2009-05-08	ARS1603, ARS1608, ARS1611, ARS1612, ARS1617, ARS1620, ARS1629, ARS1632 The following ARS elements on Chromosome 16 were added to the genome annotation based on Raveendranathan et al. 2006: ARS1603, ARS1608, ARS1611, ARS1612, ARS1617, ARS1620, ARS1629, and ARS1632. 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. SGD paper | PubMed | Full-Text
2007-07-10	YPR153W The start of ORF YPR153W was moved 122 nt upstream and an intron was added at relative coordinates 6..139 based on GenBank EF123126, Juneau et al. 2007, Zhang et al. 2007, and Miura et al. 2006. According to Juneau et al. 2007, the intron is "inefficiently spliced" (splicing rate 50%). The ORF had been annotated as 435 nt long (144 aa), but is now 557 nt long with a 134-nt intron (140 aa). Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. SGD paper | PubMed | Full-Text Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7. SGD paper | PubMed | Full-Text Zhang Z, et al. (2007) Genome-wide identification of spliced introns using a tiling microarray. Genome Res 17(4):503-9. SGD paper | PubMed | Full-Text | YFGdb
2007-05-09	YPR010C-A YPR010C-A added as a new ORF on ChrXVI between tRNA-Lys and YPR011C. Contains an intron and is conserved among all the Saccharomyces sensu stricto species. Ken Wolfe's lab found a conserved homolog in Kluyveromyces polysporus, without an intron. Note: Miura et al. refer to this as "transcription unit no. 633". Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. SGD paper | PubMed | Full-Text
2007-05-09	snR70 Updated coordinates of snR70 based on GenBank AF064282. Removed 1 nt from 5' end.
2007-04-04	YPL230W YPL230W mRNA contains an intron in the 5' untranslated region (UTR). Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. SGD paper | PubMed | Full-Text
2006-10-04	ARS1633, ARS1634, ARS1635 The following ARS elements on Chromosome XVI were added to SGD based on Nieduszynski et al. 2006: ARS1633/1620.5, ARS1634/1622.5, ARS1635/1626.5. Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. SGD paper | PubMed | Full-Text | Web Supplement
2006-09-08	ARS1604, ARS1605, ARS1607, ARS1614, ARS1618, ARS1619, ARS1621, ARS1622, ARS1623, ARS1624, ARS1625, ARS1626, ARS1627, ARS1628, ARS1630, ARS1631 The following new ARS elements on Chromosome XVI were added to SGD based on Nieduszynski et al. 2006: ARS1604, ARS1605, ARS1607, ARS1614, ARS1618, ARS1619, ARS1621, ARS1622, ARS1623, ARS1624, ARS1625, ARS1626, ARS1627, ARS1628, ARS1630, ARS1631. Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. SGD paper | PubMed | Full-Text | Web Supplement
2006-05-09	CEN16 The previously annotated 3' boundary of CEN16 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. SGD paper | PubMed | Full-Text Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68. SGD paper | PubMed | Full-Text
2005-12-14	YPL052W, YPL052W-A Palanimurugan et al. 2004 have shown that the translation start site of OAZ1/YPL052W is located at chromosomal coordinate 458796, 274 bp upstream from the originally annotated start site. This change results in a merge of upstream ORF YPL052W-A into OAZ1/YPL052W. The full translation product is generated by translational frameshifting to skip the first base of what was previously annotated as the stop codon of YPL052W-A. Palanimurugan R, et al. (2004) Polyamines regulate their synthesis by inducing expression and blocking degradation of ODC antizyme. EMBO J 23(24):4857-67. SGD paper | PubMed | Full-Text
2005-12-13	YPL052W-A Based on comparisons of the genome sequences of six Saccharomyces species, Cliften et al. 2003 suggested that this new ORF, YPL052W-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. SGD paper | PubMed | Full-Text | Web Supplement
2005-12-01	YPR169W The work of Zhang & Dietrich 2005 confirmed the suggestion from Kellis et al. 2003 that the start site of YPR169W be moved 66 nt downstream from 878620 to 878686. This annotation change results in a predicted protein of 492 aa, as opposed to the previously annotated 514 aa. Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51. SGD paper | PubMed | Full-Text | YFGdb
2005-11-21	YPR145C-A Based on comparisons of the genome sequences of six Saccharomyces species, Cliften et al. 2003 suggested that this new ORF, YPR145C-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. SGD paper | PubMed | Full-Text | Web Supplement
2004-10-12	CEN16 Centromeric DNA elements CDEI, CDEII, and CDEIII were annotated based on Wieland et al. 2001 and Espelin et al. 2003. Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60. SGD paper | PubMed | Full-Text Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68. SGD paper | PubMed | Full-Text
2004-04-01	RUF6 Feature annotation removed per John McCutcheon and Sean Eddy. McCutcheon JP and Eddy SR (2004) Detailed correction to: Computational identification of noncoding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res. 31:4119-4128, 2003. SGD paper | PubMed | Full-Text
2004-01-09	YPL094C Start moved 27 bp downstream; protein is actually 274 aa rather than the previously annotated 283 aa. This is an annotation change only; no sequence change. See Willer et al. This change was also suggested by Kellis et al. based on the automated comparison of closely related Saccharomyces species. Willer M, et al. (2003) Identification of novel protein-protein interactions at the cytosolic surface of the Sec63 complex in the yeast ER membrane. Yeast 20(2):133-48. SGD paper | PubMed | Full-Text Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata
2003-09-27	YPL109C Based on the alignment of orthologs in related fungi, Cliften et al. and Brachat et al. both proposed an intron and new 3' exon for YPL109C. The resulting ORF is 47 residues longer and has an altered C-terminus. This proposal was reviewed and accepted by SGD curators. 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. SGD paper | PubMed | Full-Text Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-27	YPR098C Based on the alignment of orthologs in related fungi, Cliften et al. and Brachat et al. both proposed an intron and new 5' exon for YPR098C. The resulting ORF is in the same frame, but has a 53-residue extension at the N-terminus. This change was reviewed and accepted by SGD curators. 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. SGD paper | PubMed | Full-Text Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPR047W Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for MSF1/YPR047W be moved 15 nt (5 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) This protein is predicted to have a function in mitochondria and using the new 5' coordinate in prediction programs (MITOP and Predator) still results in a strong prediction that Msf1p will be targeted to the mitochondria. Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPR085C The automated comparison of closely related Saccharomyces species suggests that the start site for YPR085C be moved 15 nt (5 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. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPL270W Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for MDL2/YPL270W be moved 141 nt (47 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) Although a corresponding ATG is found at the original start (30341) in S. paradoxus, S. mikatae, and S. bayanus, there are indels between this ATG and the predicted start site which lead to frameshifts in the predicted mRNAs in non S. cerevisiae sequences. 4) the protein is found in mitochondria (Young et al.) and the MITPROT prediction program predicts a signal cleavage site for the new shorter protein suggesting this protein would be targeted to the mitochondria. In contrast, mitochondrial targeting is not predicted with the protein's original start at 30341. Young L, et al. (2001) Role of the ABC transporter Mdl1 in peptide export from mitochondria. Science 291(5511):2135-8. SGD paper | PubMed | Full-Text Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPR093C The automated comparison of closely related Saccharomyces species suggests that the start site for YPR093C be moved 66 nt (22 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. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPL210C Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for SRP72/YPL210C be moved 18 nt (6 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 at 156229 is not conserved in the other Saccharomyces species; 4) Protein sequence comparisons against the nr dataset show that sequence similarity begins after 156211 between S. cerevisiae YPL210C and related proteins. Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPR175W Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for DPB2/YPR175W be moved 9 nt (3 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 at 888960 is not conserved in S. paradoxus, S. mikatae, and S. bayanus. Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-22	YPL148C Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for PPT2/YPL148C be moved 12 nt (4 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. SGD paper | PubMed | Full-Text | Comments & Errata Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-09-09	TEL16L, TEL16R The chromosomal locations for TEL16L, TEL16L-XC, TEL16L-XR, TEL16L-YP, TEL16R, TEL16R-XC, and TEL16R-YP were generously provided by Ed Louis and Dave Barton (University of Leicester, UK). Note that both TEL16L and TEL16R have telomeric repeats (TEL16L-TR and TEL16R-TR), but they are missing from the genome annotation due to sequencing difficulties encountered during the initial genome sequencing efforts in the 1990s.
2003-07-29	YPL189C-A Thanks to Brachat et al. for providing the coordinates of YPL189C-A. 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. SGD paper | PubMed | Full-Text
2003-07-29	YPR170W-B Thanks to Brachat et al. for providing the coordinates of YPL189C-A. 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. SGD paper | PubMed | Full-Text Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. SGD paper | PubMed | Full-Text | Web Supplement
2003-07-29	YPL135C-A, YPL152W-A, YPL222C-A, YPL283W-A, YPL283W-B, YPR159C-A, YPR160C-A, YPR204C-A Thanks to Kumar et al. for providing the coordinates of the following Chromosome XVI ORFs: YPL152W-A, YPL222C-A, YPL283W-A, YPL283W-B, YPR159C-A, YPR160C-A, YPR204C-A, and YPL135C-A. Kumar A, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63. SGD paper | PubMed | Full-Text | YFGdb | Comments & Errata
2003-07-29	YPL038W-A, YPL250W-A, YPR108W-A, YPR169W-A Thanks to Kessler et al. for providing the coordinates of the following Chromosome XVI ORFs: YPR169W-A, YPR108W-A, YPL038W-A, and YPL250W-A. Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71. SGD paper | PubMed | Full-Text
2003-07-29	YPL119C-A, YPR160W-A, YPR170W-A Thanks to Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome XVI ORFs: YPR170W-A, YPL119C-A and YPR160W-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. SGD paper | PubMed | Full-Text Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51. SGD paper | PubMed | Full-Text | YFGdb Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20. SGD paper | PubMed | Full-Text | Web Supplement | YFGdb
2003-05-23	YPR131C The start site of NAT3/YPR131C has been moved 168 nt downstream from 794661 to 794493 based on experimental evidence as well as sequence comparisons in other species published by Polevoda et al. Also, the downstream ATG codon is clearly conserved in the closely related sensu stricto Saccharomyces species. Polevoda B, et al. (2003) Nat3p and Mdm20p are required for function of yeast NatB Nalpha-terminal acetyltransferase and of actin and tropomyosin. J Biol Chem 278(33):30686-97. SGD paper | PubMed | Full-Text
2003-03-06	RUF6 Thanks to John McCutcheon and Sean Eddy for providing the coordinates for the following RNA features: SNR82, SNR83, SNR84, RUF4, RUF5-1, RUF5-2, RUF6, RUF7, and RUF8. McCutcheon JP and Eddy SR (2003) Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 31(14):4119-28. SGD paper | PubMed | Full-Text
2002-07-25	YPR036W-A Based on the work of Miura et al. (2001), the new ORF YPR036W-A was added to Chromosome XV. Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51. SGD paper | PubMed | Full-Text
1999-07-17	YPR111W The intron in ORF YPR111W was removed. The start, stop, and frame were left as is, so that the sequence that was previously annotated as the intron is now part of the translation. The chromosomal coordinates of the coding region change from 747303-747593..748014-748997 to 747303-748997. The relative coordinates of the coding region change from 1-291..712-1695 to 1-1695.
1998-05-21	YPR002C-A The following 27 ORFs were added to the genome annotation based on Velculescu et al. 1997: YBL091C-A, YBL107W-A, YCR018C-A, YCR102W-A, YDL130W-A, YDR034C-A, YDR034W-B, YDR363W-A, YDR525W-A, YER048W-A, YER091C-A, YER138W-A, YGR122C-A, YIR020W-B, YKL033W-A, YKL053C-A, YKL162C-A, YLL018C-A, YLR262C-A, YML081C-A, YMR046W-A, YMR158C-B, YMR194C-A, YNR032C-A, YOL013W-A, YOR298C-A, and YPR002C-A. The coordinates of the tag sequences along the genome were determined and each tag was classified into one of these four categories: 1) class 1 - within an existing ORF, 2) class 2 - within 500 bp downstream of existing an ORF, 3) class 4 - opposite of an existing ORF, or 4) class 3 - none of the above. The regions between two existing ORFs which contained one or more unique class 3 tags (number 4) above) were examined for potential coding sequences in which the unique tag was located either within the coding sequence or 500bp downstream of this sequence. BLASTP analysis was then performed for each potential ORF meeting these criteria against the non-redundant (nr) NCBI dataset, and those with a P value exponent of -6 or less were analyzed further. The BLAST results were analyzed on an individual basis for each potential ORF meeting the above criteria. Those potential ORFs which exhibited reasonable homology to other proteins, and did not appear to be matched with other proteins based on homology to repetitive sequences alone, were identified and entered into SGD. Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51. SGD paper | PubMed | Full-Text | YFGdb
1997-10-20	YPL075W Edition 14: The GCR1 gene was modified in October 1997 to include an intron reported by Tornow and Santangelo (1994). Tornow J and Santangelo G (1994) The GCR1 gene of Saccharomyces cerevisiae is a split gene with an unusually long intron. Genetics 138(3):973-4. SGD paper | PubMed | Full-Text Cherry JM, et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387(6632 Suppl):67-73. SGD paper | PubMed | Full-Text