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Chromosome XVI History Help



 

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.


SEQUENCE CHANGES, including any resulting annotation changesJump to: Annotation changes

DateAffected FeaturesStart Coordinate
of Change
End Coordinate
of Change
Type of ChangeOld SequenceNew Sequence
2011-02-03
YPL224C
126768126768Insertion C
128039128039SubstitutionTG
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2004-07-21
YPL109C
347265347265DeletionT
347273347273InsertionT
347285347285InsertionA
347375347375InsertionT
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2011-02-03
YPL108W, YPL109C
347528347528Insertion G
347759347759Insertion 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YPL036W, YPL037C482773482773DeletionT
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03
YPL016W, YPL017C
520375520375Insertion C
520378520378SubstitutionCG
520646520646Insertion C
520818520818DeletionT
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YPL016W523639523639SubstitutionCT
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03
YPR035W
642955642955SubstitutionGA
642995642995SubstitutionCT
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YPR035W, YPR036W643579643579SubstitutionTC
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YPR078C, YPR079W698524698524DeletionA
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2003-09-29YPR089W, YPR090W713683713683DeletionT
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2011-02-03YPR097W727933727933SubstitutionGA
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03
YPR121W, YPRWdelta16
778302778302Insertion G
778376778376Insertion C
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YPR121W778863778863SubstitutionTA
 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. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

ANNOTATION CHANGES without sequence changesJump to: Sequence changes

Date Affected Features
2009-05-08ARS1603, 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 Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2007-07-10YPR153W
 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  
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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  yfgdb  
Zhang Z, et al. (2007) Genome-wide identification of spliced introns using a tiling microarray. Genome Res 17(4):503-9
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  yfgdb  

2007-05-09YPR010C-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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  

2007-05-09snR70
 Updated coordinates of snR70 based on GenBank AF064282. Removed 1 nt from 5' end.
2007-04-04YPL230W
 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  

2006-10-04ARS1633, 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  

2006-09-08ARS1604, 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  

2006-05-09CEN16
 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 Papers Entry  Pubmed Entry  PMC full text  DOI 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2005-12-14YPL052W, 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 Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2005-12-13YPL052W-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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2005-12-01YPR169W
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  yfgdb  

2005-11-21YPR145C-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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2004-10-12CEN16
 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 Papers Entry  Pubmed Entry  PMC full text  DOI 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2004-04-01RUF6
 Feature annotation removed per John McCutcheon and Sean Eddy.

McCutcheon J and Eddy S (2004) Corrigendum: Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res 32 (15):4713
SGD Papers Entry  

2004-01-09YPL094C
 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 Papers Entry  Pubmed Entry  DOI 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata

2003-09-27YPR098C
 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-27YPL109C
 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 Papers Entry  Pubmed Entry  PMC full text  DOI full text  
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPL210C
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPR093C
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPR085C
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPL270W
 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 Papers Entry  Pubmed Entry  DOI 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
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2003-09-22YPR047W
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPR175W
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YPL148C
 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 Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-09TEL16L, TEL16L-XC, TEL16L-XR, TEL16L-YP, TEL16R, TEL16R-XC, TEL16R-YP
 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.
2003-07-29YPR170W-B
 Thanks to Brachat et al and Cliften et al. for providing the coordinates of YPR170W-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
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Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
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2003-07-29YPL135C-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
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2003-07-29YPL189C-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
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2003-07-29YPL119C-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
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Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51
SGD Papers Entry  Pubmed Entry  DOI full text  yfgdb  
Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20
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2003-07-29YPL038W-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
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2003-05-23YPR131C
 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
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2003-03-06RUF6
 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
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2002-07-25YPR036W-A
 Based on the work of Miura et al. (2001), the new ORF YPR036W-A was added to Chromosome XV.

Miura F, et al. (2001) Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast. FEBS Lett 505(1):103-8
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1999-07-17YPR111W
 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.
1998-05-21YPR002C-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 Papers Entry  Pubmed Entry  DOI full text  yfgdb  

1997-10-20YPL075W
 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
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Cherry JM, et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387(6632 Suppl):67-73
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