Difference between revisions of "Chromosome XV History"

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(→‎Sequence Changes)
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Old: 42507 AAGGTATACCGTCGGAAATTCCGTGGCAG-TTTACAGGCC 42545</pre>
 
Old: 42507 AAGGTATACCGTCGGAAATTCCGTGGCAG-TTTACAGGCC 42545</pre>
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2006-01-05
 +
| [https://www.yeastgenome.org/locus/YOR252W YOR252W]
 +
| 803745
 +
| 803745
 +
| Insertion
 +
|
 +
| G
 +
|-
 +
| || colspan="6" | SGD confirmed the sequence error predicted by the work of Kellis, et al, and have updated the systematic sequence accordingly.
 +
<pre>New: 803730 ACGGTTCATCCGAAGGGTAGAAAGTATGAAAAGCT 803764
 +
            |||||||||||||||| ||||||||||||||||||
 +
Old: 803730 ACGGTTCATCCGAAGG-TAGAAAGTATGAAAAGCT 803763</pre>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata]<br>
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2004-02-13
 +
| [https://www.yeastgenome.org/locus/YOR298C-A YOR298C-A]
 +
| 877622
 +
| 877622
 +
| Insertion
 +
|
 +
| GC
 +
|-
 +
| || colspan="6" | Two nucleotides GC were inserted after the G at coordinate 877622 in what had previously been annotated as the intergenic region between YOR298C-A and YOR299W. This region is now part of YOR298C-A, as the start for this ORF was moved 279 bp upstream from 877403 to 877682 (note that YOR298C-A is encoded on the Crick strand). As a result, YOR298C-Ap was increased from 58 aa to 151 aa. See Brachat et al. 2003 and GenBank AY260886. This change was also predicted by Kellis et al. and Cliften et al.
 +
<pre>Query:    361 AATTTGGCCTTGAGATCTGGCAACGTTGGCCCTTGGGCCAGAACCACCAGCTCTTGCTCT 420             
 +
              ||||||||||||||||||||||||||||||||||||  ||||||||||||||||||||||
 +
Sbjct: 877587 AATTTGGCCTTGAGATCTGGCAACGTTGGCCCTTGG--CAGAACCACCAGCTCTTGCTCT 877644</pre>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata]<br>
 +
'''Brachat S, et al.''' (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45. <br>
 +
[https://www.yeastgenome.org/reference/S000073670 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12844361 PubMed] | [https://genomebiology.biomedcentral.com/articles/10.1186/gb-2003-4-7-r45 Full-Text]<br>
 +
'''Cliften P, et al.''' (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6. <br>
 +
[https://www.yeastgenome.org/reference/S000073948 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12775844 PubMed] | [https://science.sciencemag.org/content/301/5629/71.long Full-Text] | [https://science.sciencemag.org/content/suppl/2003/07/03/1084337.DC1 Web Supplement] <br>
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2003-01-09
 +
| [https://www.yeastgenome.org/locus/YOR087W YOR087W], [https://www.yeastgenome.org/locus/YOR088W YOR088W]
 +
| 488439
 +
| 488439
 +
| Insertion
 +
|
 +
| T
 +
|-
 +
| || colspan="6" | Due to the insertion of a T after the A at 488439 on chromosome 15, YOR087W and YOR088W have been merged to one single ORF - YVC1/YOR087W, with YOR088W as an alias. The old chromosomal coordinates for YOR087W were 487708-488451, and for YOR088W were 488286-489734. The new chromosomal coordinates for the fused ORF are 487708-489735. The old relative coordinates for YOR087W were 1-744, and for YOR088W were 1-1449. The new relative coordinates for the fused ORF are 1-2028.<br><br>
 +
'''Denis V and Cyert MS''' (2002) Internal Ca(2+) release in yeast is triggered by hypertonic shock and mediated by a TRP channel homologue. J Cell Biol 156(1):29-34.<br>
 +
[https://www.yeastgenome.org/reference/S000069157 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11781332 PubMed] | [http://jcb.rupress.org/content/156/1/29.long Full-Text] <br>
 +
'''Palmer CP, et al.''' (2001)  A TRP homolog in Saccharomyces cerevisiae forms an intracellular Ca(2+)-permeable channel in the yeast vacuolar membrane. Proc Natl Acad Sci U S A 98(14):7801-5. <br>
 +
[https://www.yeastgenome.org/reference/S000069248 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11427713 PubMed] | [https://www.pnas.org/content/98/14/7801.long Full-Text] <br>
 +
'''Kellis M, et al.''' (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54. <br>
 +
[https://www.yeastgenome.org/reference/S000073327 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12748633 PubMed] | [https://www.nature.com/articles/nature01644 Full-Text] | [https://www.yeastgenome.org/reference/S000140268 Comments & Errata]<br>
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2001-05-31
 +
| [https://www.yeastgenome.org/locus/YOR068C YOR068C], [https://www.yeastgenome.org/locus/YOR069W YOR069W]
 +
| 453804
 +
| 453804
 +
| Insertion
 +
|
 +
| G
 +
|-
 +
| || colspan="6" | Inserted one G nucleotide after the G at chromosomal coordinate 453805, in the intergenic region to the left of overlapping ORFs YOR068C and YOR068W:
 +
<pre>Old: 453752 ATCCTGCAATAACAAGCCATGGACTACGAGGATAATCTAGAAGCACCTGTTTGG-ACGAA 453810
 +
            |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
 +
New: 453752 ATCCTGCAATAACAAGCCATGGACTACGAGGATAATCTAGAAGCACCTGTTTGGGACGAA 453811</pre>
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 1997-08-11
 +
| [https://www.yeastgenome.org/locus/YOL025W YOL025W]
 +
| 276609
 +
| 276609
 +
| Substitution
 +
| G
 +
| A
 +
|-
 +
| || colspan="6" | A single nucleotide substitution was made in the systematic sequence in the region covering the ORF LAG2/YOL025W. The G at 276609 was changed to an A.
 +
<pre>New: 276601 AAAGCAGGAAATTTTACCCAAAAAATTGATGAAGGAGTGACCTTAAGAACAATGATTCTT 276660
 +
            |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
 +
Old: 276601 AAAGCAGGGAATTTTACCCAAAAAATTGATGAAGGAGTGACCTTAAGAACAATGATTCTT 276660</pre>
 +
 +
|}
 +
 +
<br><br>
 +
 +
=Annotation Changes ''without sequence changes''=
 +
{| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
 +
! Date  !! Affected Features

Revision as of 14:51, 2 October 2019

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

  • The sequence of Chromosome XV has been updated 63 times, affecting 53 features.
  • The annotation of Chromosome XV has been updated 51 times, affecting 90 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 YOL138C 64173 64173 Substitution G C
61985 61985 Substitution A T
63708 63708 Substitution C T
Nucleotide change(s) in the coding region of RTC1/YOL138C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 393 is now Cysteine rather than Serine, and residue 548 is now Aspartic Acid rather than Glycine. 
New    61970    CGCATGTCTGGGCGATCCGATTATTGGTGCTGTATGGGAAGAAAGCTTTTTAAAAGTTTC  62029
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old    61970    CGCATGTCTGGGCGAACCGATTATTGGTGCTGTATGGGAAGAAAGCTTTTTAAAAGTTTC  62029

New    63660    GTAGGTTGAAGCTCCGGTTCTACCACCTCATATGAGCCTATCTCTTGGTCAACTGAAAGT  63719
                |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Old    63660    GTAGGTTGAAGCTCCGGTTCTACCACCTCATATGAGCCTATCTCTTGGCCAACTGAAAGT  63719

New    64140    GCATTGGCATTGTCGCCAACAAACCAGAGGCAGCATTTACCGTCTCTACCACCTGTAGCA  64199
                ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
Old    64140    GCATTGGCATTGTCGCCAACAAACCAGAGGCAGGATTTACCGTCTCTACCACCTGTAGCA  64199

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 YOL142W 56036 56036 Substitution C G
Nucleotide change(s) in the coding region of RRP40/YOL142W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 160 is now Leucine rather than Phenylalanine. 
New    55991    CTGGTTTCGGGATATTGGAAGATGGTATGATCATTGACGTGAATTTGAATTTCGCACGCC  56050
                |||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Old    55990    CTGGTTTCGGGATATTGGAAGATGGTATGATCATTGACGTGAATTTCAATTTCGCACGCC  56049

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 YOL077C 186243 186243 Substitution A C
Nucleotide change(s) in the coding region of BRX1/YOL077C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 161 is now Glycine rather than Cysteine. 
New    186230   TTTGGTGGTACACCAAAATTATGCACTAGCAACTCCTTAATTAATTGGTAGTGTGGGGAG  186289
                ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Old    186230   TTTGGTGGTACACAAAAATTATGCACTAGCAACTCCTTAATTAATTGGTAGTGTGGGGAG  1862890

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 YOL075C 190052 190052 Substitution CG GC
Nucleotide change(s) in the coding region of YOL075C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 1164 is now Alanine rather than Arginine. 
New    190020   TTTCGAAAAATGTATTTGTCATTATACCAAGAGCTTCGCCACAACAGGTAACAATAAAGG  190079
                ||||||||||||||||||||||||||||||||  ||||||||||||||||||||||||||
Old    190020   TTTCGAAAAATGTATTTGTCATTATACCAAGACGTTCGCCACAACAGGTAACAATAAAGG  190079

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 YOR306C 889947 889947 Substitution G C
Nucleotide change(s) in the coding region of MCH5/YOR306C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 495 is now Cysteine rather than Serine. 
New    889913   ATGTAGCAAACAGCGCTTACAAAAGTTGCCAAACCGCAAAAAATAATATAGTGTTGGTAA  889972
                |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Old    889911   ATGTAGCAAACAGCGCTTACAAAAGTTGCCAAACCGGAAAAAATAATATAGTGTTGGTAA  889970

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 YOR149C 611036 611036 Substitution A G
611023 611024 Substitution GC TG
Nucleotide change(s) in the coding region of SMP3/YOR149C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 122-123 are now IK rather than MQ. 
New    610993   TACGTAAGAAGTTAAAAGTAGACTTTTTTTGATGAATTGTACGGCCTTTCTCTCATCCCT  611052
                |||||||||||||||||||||||||||||  ||||||||||| |||||||||||||||||
Old    610994   TACGTAAGAAGTTAAAAGTAGACTTTTTTGCATGAATTGTACAGCCTTTCTCTCATCCCT  611053

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 YOR140W 588363 588365 Substitution GCG AGC
588344 588344 Deletion C
588318 588318 Insertion T
Nucleotide change(s) in the coding region of SFL1/YOR140W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 446-462 are now FVQYQPQSQQHVTYAKQ rather than LYNTNRSRNQHVTYASE. 
New    588314   TTTTTGTACAATACCAACCGCAGTCGCAAC-AACATGTGACTTATGCGAAGCAACCGGCA  588372
                |||| ||||||||||||||||||||||||| ||||||||||||||||||   ||||||||
Old    588315   TTTT-GTACAATACCAACCGCAGTCGCAACCAACATGTGACTTATGCGAGCGAACCGGCA  588373

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 YOL058W 220195 220195 Deletion T
220207 220207 Insertion C
Nucleotide change(s) in the coding region of ARG1/YOL058W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 329-332 are now SYFT rather than FLLH. 
New    220179   TTGATATATAACGGTT-CCTACTTCACCCCAGAGTGTGAGTACATCAGATCTATGATCCA  220238
                |||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||
Old    220179   TTGATATATAACGGTTTCCTACTTCACCC-AGAGTGTGAGTACATCAGATCTATGATCCA  220237

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 YOR130C 570495 570495 Substitution A G
Nucleotide change(s) in the coding region of ORT1/YOR130C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 105 is now Serine rather than Phenylalanine. 
New    570474   TCAGGATTTGCCCCAACGGGGAAACGTTTGTATGTTTTTCTAAAAATTTAGAACATTGGT  570533
                |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Old    570475   TCAGGATTTGCCCCAACGGGAAAACGTTTGTATGTTTTTCTAAAAATTTAGAACATTGGT  570534

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 YOR297C 874911 874911 Substitution C T
Nucleotide change(s) in the coding region of TIM18/YOR297C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 137 is now Glutamic Acid rather than Glycine. 
New    874863   TCCTCCATAGAGGCAATAAAGGGCGAGCTTATGCCATCTTGGATACTTTTCCTTCGGTAT  874922
                ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Old    874862   TCCTCCATAGAGGCAATAAAGGGCGAGCTTATGCCATCTTGGATACTTTCCCTTCGGTAT  874921

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 YOL022C 280393 280393 Substitution A G
A single nucleotide substitution was made within ORF TSR4/YOL022C. Note that the protein sequence was not changed. 
New    280377   GGTACCCCATTCCATGCCGTTATCGACAGACACTACTTCTTCCAGATCAAAAATCATCTT  280436
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old    280378   GGTACCCCATTCCATACCGTTATCGACAGACACTACTTCTTCCAGATCAAAAATCATCTT  280437

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 YOR255W, YOR256C 808197 808197 Insertion A
A single nucleotide insertion was made in the intergenic region between ORFs OSW1/YOR255W and TRE2/YOR256C. 
New    808183   TTACATAATTAAAGAAAAAATTTTATTAACATACTTCCTTATACTTACAATATGTATTCT  808242
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old    808184   TTACATAATTAAAG-AAAAATTTTATTAACATACTTCCTTATACTTACAATATGTATTCT  808242

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 YOR298C-A, YOR299W 877795 877795 Insertion G
A single nucleotide insertion was made in the intergenic region between ORFs MBF1/YOR298C-A and BUD7/YOR299W. 
New    877783   CTATTATTGGTTAAGCGACAGGCGCCTTTCCAGCTACCTAATATATACCACCACCGTCAA  877842
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old    877782   CTATTATTGGTTAA-CGACAGGCGCCTTTCCAGCTACCTAATATATACCACCACCGTCAA  877840

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 ARS1531 35765 35765 Substitution G C
A single nucleotide substitution was made within ARS1531. 
New    35751    TTTTCAAAATCCGCGCAAAATTATAGAATTCATCATATATAATGAAGGAACTGTGTTCCT  35810
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old    35750    TTTTCAAAATCCGCGGAAAATTATAGAATTCATCATATATAATGAAGGAACTGTGTTCCT  35809

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

2004-01-23 ARS1531, YOL152W 36149 36149 Substitution G A
36119 36119 Substitution G C
36056 36056 Substitution G A
36013 36013 Substitution T A
Four separate single nucleotide substitutions were made in the intergenic region between ARS1531 and ORF FRE7/YOL152W. 
New    36001    AAAACTTGAGAATAACATAACCCTTTAATAGGCCAATGCAACTGATAGAACACCAGAAAA  36060
                ||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |||
Old    36000    AAAACTTGAGAATTACATAACCCTTTAATAGGCCAATGCAACTGATAGAACACCAGGAAA  36059
New    36061    AGTTGTAATGCCAGTGCGGCTGAACAGAATCTGTGGTAATAGATTTCGGGTATAATGCGC  36120
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    36060    AGTTGTAATGCCAGTGCGGCTGAACAGAATCTGTGGTAATAGATTTCGGGTATAATGCGG  36119
New    36121    AAATTAGGAATACTCATATGTTCAGATAGAATAAATAATAAAGAGACCTTCAACATAAAA  36180
                ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old    36120    AAATTAGGAATACTCATATGTTCAGATAGGATAAATAATAAAGAGACCTTCAACATAAAA  36179

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 YOR256C 809751 809751 Substitution C T
A single nucleotide substitution was made within ORF TRE2/YOR256C. Note that the protein sequence was not changed. 
New    809693   GTCTATATTCTCACCATATGGCTCAGATATGAAGATTACAGCTTTAGCTCCGAATTTCTC  809762
                |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Old    809693   GTCTATATTCTCACCATATGGCTCAGATATGAAGATTACAGCTTTAGCCCCGAATTTCTC  809762

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 YOL125W 84121 84121 Substitution T C
A single nucleotide substitution was made within ORF TRM13/YOL125W. 
New    84110    AAAAAATGCAACAAGACCAAACTAAGCCATTTAAACGATGATAAGCCATACTATGAACCG  84169
                ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Old    84110    AAAAAATGCAATAAGACCAAACTAAGCCATTTAAACGATGATAAGCCATACTATGAACCG  84169

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 YOL058W, YOL059W 219000 219000 Insertion G
A single nucleotide insertion was made in the intergenic region between ORFs GPD2/YOL059W and ARG1/YOL058W. 
New    218990   ATGACTGCGTAGCGGCAGATAGTGTAATCTGAGCAGTTGCGAGACCCAGACTGGCACTGT  219049
                ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Old    218990   ATGACTGCGTA-CGGCAGATAGTGTAATCTGAGCAGTTGCGAGACCCAGACTGGCACTGT  219048

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 YOL036W, snR50 259235 259235 Deletion A
259230 259230 Deletion T
Two single nucleotide deletions were made in the intergenic region between ORF YOL036W and snoRNA SNR50. 
New    259199   ATTAGGATGGTAGCCCTACCTTTTTTTTTTTT-GGCA-CACATGGTCAACTTTTCTTCTC  259256
                |||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||
Old    259198   ATTAGGATGGTAGCCCTACCTTTTTTTTTTTTTGGCAACACATGGTCAACTTTTCTTCTC  259257

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 YOR106W, YOR107W 521099 521099 Deletion C
521071 521071 Insertion A
A single nucleotide insertion and a single nucleotide deletion were made in the intergenic region between ORFs VAM3/YOR106W and RGS2/YOR107W. 
New    521055   TGGAGATGAAAAAAAAACTTGCTGAATAAAGATAGTTAAGGCGC-TAGTAATCAAATTAA  521113
                |||||||||||||||| ||||||||||||||||||||||||||| |||||||||||||||
Old    521056   TGGAGATGAAAAAAAA-CTTGCTGAATAAAGATAGTTAAGGCGCCTAGTAATCAAATTAA  521114

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 YOR090C, YOR091W 492979 492979 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs PTC5/YOR090C and TMA46/YOR091W. 
New    492955   TACCCTCCAATCGATCCTTTTTTTCTTTTTTGTATCTTGTGTAGAAAGAAGTGAATCCTG  493014
                ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Old    492957   TACCCTCCAATCGATCCTTTTTT-CTTTTTTGTATCTTGTGTAGAAAGAAGTGAATCCTG  493015

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 YOL145C 52199 52199 Substitution C T
50767 50767 Substitution C T
50430 50431 Substitution GG CC
50081 50081 Substitution T C
50069 50069 Substitution G T
49941 49941 Substitution G T
49922 49922 Substitution T A
49919 49919 Substitution A T
49912 49912 Substitution A T
49829 49829 Substitution G T
Several nucleotide changes were made in the coding region of CTR9/YOL145C, resulting in an altered protein sequence. The start, stop, and reading frame remain the same, but with the following changes: Gly197->Lys, Gly674->Glu, Thr786->Arg, Lys903->Glu, Arg907->Ser, residues 956-959 are now LIQE not IFQV, and Glu987->Lys. 
New    49811    GTCTTGGCTTTTCTTCGTCATATTCATTGTCTTTATCAGACAGATCTGAA  49870
                ||||||||| ||||||||||||||||||||||||||||||||||||||||
Old    49820    GTCTTGGCTGTTCTTCGTCATATTCATTGTCTTTATCAGACAGATCTGAA  49869
New    49871    TCATCTTTAACATTATGTTCACTTATGGCCATGGCTTCTCGCTCCTGGAT  49920
                |||||||||||||||||||||||||||||||||||||||||| ||||||
Old    49870    TCATCTTTAACATTATGTTCACTTATGGCCATGGCTTCTCGCACCTGGAA  49919
New    49921    TAACTTTTGTGCCTCATCTTGTAGTTTCCTATACTCCTCTGCCTGTTTTT  49970
                || |||||||||||||||||| ||||||||||||||||||||||||||||
Old    49920    TATCTTTTGTGCCTCATCTTGGAGTTTCCTATACTCCTCTGCCTGTTTTT  49969
New    50041    AATTTTACGTGCTTCATCAATTTTGGCGCTTTGTTCCTTCTCAAATTCTT  50090
                ||||||||||||||||||||||||||||| ||||||||||| ||||||||
Old    50040    AATTTTACGTGCTTCATCAATTTTGGCGCGTTGTTCCTTCTTAAATTCTT  50089
New    50401    TTCCAAGGCTTTTTGATAAAAATTCACAGACCTTTCCTTAATGGCACGTG  50450
                ||||||||||||||||||||||||||||||  ||||||||||||||||||
Old    50400    TTCCAAGGCTTTTTGATAAAAATTCACAGAGGTTTCCTTAATGGCACGTG  50449
New    50761    TGATTTTTCCTGTTCCTTTGGATTCCTGGACTTTTTACCGTCTCTGGCAA  50810
                ||||||| ||||||||||||||||||||||||||||||||||||||||||
Old    50760    TGATTTTCCCTGTTCCTTTGGATTCCTGGACTTTTTACCGTCTCTGGCAA  50809
New    52161    GCAATTCTTGAAAAATTTTCAGACTGGCCATATAATTTTTCTTCTGATAA  52210
                ||||||||||||||||||||||||||||||||||||||| ||||||||||
Old    52160    GCAATTCTTGAAAAATTTTCAGACTGGCCATATAATTTTCCTTCTGATAA  52209

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 YOL140W, YOL141W 58601 58601 Substitution C G
58558 58558 Deletion T
A single nucleotide deletion and a single nucleotide substitution were made in the intergenic region between ORFs PPM2/YOL141W and ARG8/YOL140W. 
New    58550    GGATTCGA-ATGGTTGCCAGCTCGCTATGTGACTCACTTAAAGTACATGATGCGTCATTG  58609
                ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Old    58550    GGATTCGATATGGTTGCCAGCTCGCTATGTGACTCACTTAAAGTACATGATCCGTCATTG  58609

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 YOL139C, YOL140W 60173 60173 Substitution A G
A single nucleotide substitution was made in the intergenic region between ORFs ARG8/YOL140W and CDC33/YOL139C. 
New    60130    CTTACGTGATATGTACATGTGGTGCGTCTTTCATACCTTGAATGATATAATTAATAAGAG  60189
                ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Old    60130    CTTACGTGATATGTACATGTGGTGCGTCTTTCATACCTTGAATAATATAATTAATAAGAG  60189

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 YOL135C, YOL136C 69084 69084 Substitution C T
A single nucleotide substitution was made in the intergenic region between ORFs PFK27/YOL136C and MED7/YOL135C. 
New    69060    AACCGAGTAATCCAATTTACTTTTTCTACTTTTTTTTCATTATCAATCGATTCAGATGCC  69119
                |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Old    69060    AACCGAGTAATCCAATTTACTTTTCCTACTTTTTTTTCATTATCAATCGATTCAGATGCC  69119

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 YOR008C-A, YOR008W-B 343142 343142 Insertion A
A single nucleotide insertion was made in the intergenic region between ORFs YOR008C-A and YOR008W-B. 
New    343127   GAAGTATGTAAAAAAATTACACACCATTAAGTTCTTATGTAAACCGAAGTCTGGAAGAGA  343186
                ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old    343128   GAAGTATGTAAAAAA-TTACACACCATTAAGTTCTTATGTAAACCGAAGTCTGGAAGAGA  343186

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 YOR261C, YOR262W 816959 816959 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs RPN8/YOR261C and YOR262W. 
New    816943   TTTCCTTTCTTTCTTTCTTTTTTTAAATTCGAAAAATGCCCTCAATCAGTAGCAGTTGTA  817002
                ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Old    816943   TTTCCTTTCTTTCTTTC-TTTTTTAAATTCGAAAAATGCCCTCAATCAGTAGCAGTTGTA  817001

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 YOL076W, YOL077C 186978 186979 Substitution CG GC
A single nucleotide substitution was made in the intergenic region between ORFs BRX1/YOL077C and MDM20/YOL076W. 
New    186960   ACAGAATTCATTGGCGAAGCAACGATACATAACGAGCTCGGTACAGCAATCATCGCATCG  187019
                ||||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||
Old    186960   ACAGAATTCATTGGCGAACGAACGATACATAACGAGCTCGGTACAGCAATCATCGCATCG  187019

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 YOL062C, YOL063C 210486 210487 Substitution AC CA
210453 210454 Substitution AC CA
Two separate dinucleotide substitutions were made in the intergenic region between ORFs CRT10/YOL063C and APM4/YOL062C. 
New    210440   TTAACAAAATGTGCATTCTAAAGGAAATTACTATAAAAAATACAGGCATGATAAAAATAT  210499
                |||||||||||||  |||||||||||||||||||||||||||||||  ||||||||||||
Old    210440   TTAACAAAATGTGACTTCTAAAGGAAATTACTATAAAAAATACAGGACTGATAAAAATAT  210499

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 YOR306C, YOR307C 892173 892173 Insertion C
A single nucleotide insertion was made in the intergenic region between ORFs MCH5/YOR306C and SLY41/YOR307C. 
New    892133   TTTCTCTCAACCTTTCGAGTACTTGGAAAAAGGAGTAGATCCGCTTTCAGCAATCGAAGC  892192
                ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Old    892131   TTTCTCTCAACCTTTCGAGTACTTGGAAAAAGGAGTAGATCCG-TTTCAGCAATCGAAGC  892189

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 YOR354C, YOR355W 1004737 1004737 Deletion T
A single nucleotide deletion was made in the intergenic region between ORFs MSC6/YOR354C and GDS1/YOR355W. 
New    1004693  TCAGCATTCCATTATTGAAGGCTTTAAAATAATAGTTTCTTTTTTCC-TATTATTTTATT  1004751
                ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old    1004690  TCAGCATTCCATTATTGAAGGCTTTAAAATAATAGTTTCTTTTTTCCTTATTATTTTATT  1004749

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 YOR045W, YOR046C 414326 414326 Deletion T
A single nucleotide deletion was made in the intergenic region between ORFs TOM6/YOR045W and DBP5/YOR046C. 
New    414297   ATATGCTGTGTTTGTATTTATATAAGCTT-GCCTCACAAGTAAAAGTGGATCAACAAACT  414355
                ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old    414297   ATATGCTGTGTTTGTATTTATATAAGCTTTGCCTCACAAGTAAAAGTGGATCAACAAACT  414356

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 YOL163W, YOL164W 8476 8476 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs BDS1/YOL164W and YOL163W. 
New    8461     AGAGCTTTTCGTATATTCTGTTTTCCTAATAACATTTACTATTGTGAATTGAAATTTAAA  8520
                |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||
Old    8461     AGAGCTTTTCGTATAT-CTGTTTTCCTAATAACATTTACTATTGTGAATTGAAATTTAAA  8519

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 YOR049C, YOR050C 423752 423752 Deletion T
A single nucleotide deletion was made in the intergenic region between ORFs RSB1/YOR049C and YOR050C. 
New    423716   CGAAGGTTCGGTACCATACCACCATAAAGGGAATT-ACTGTTAGCTGCTGCTTCTAACTG  423774
                ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Old    423717   CGAAGGTTCGGTACCATACCACCATAAAGGGAATTTACTGTTAGCTGCTGCTTCTAACTG  423776

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

2006-01-05 YOL152W 42535 42535 Insertion G
A sequencing error was demonstrated in BY4741 (a derivative of S288C) by Mark Rinnerthaler and Michael Breitenbach, and SGD has updated the sequence accordingly. As a consequence of this change, the stop codon has been moved 27 nts upstream, shortening the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 629 to 620 amino acids. (Personal communication from MIPS, Mark Rinnerthaler and Michael Breitenbach) 
New: 42507 AAGGTATACCGTCGGAAATTCCGTGGCAGGTTTACAGGCC 42546
           ||||||||||||||||||||||||||||| ||||||||||
Old: 42507 AAGGTATACCGTCGGAAATTCCGTGGCAG-TTTACAGGCC 42545
2006-01-05 YOR252W 803745 803745 Insertion G
SGD confirmed the sequence error predicted by the work of Kellis, et al, and have updated the systematic sequence accordingly. 
New: 803730 ACGGTTCATCCGAAGGGTAGAAAGTATGAAAAGCT 803764
            |||||||||||||||| ||||||||||||||||||
Old: 803730 ACGGTTCATCCGAAGG-TAGAAAGTATGAAAAGCT 803763

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

2004-02-13 YOR298C-A 877622 877622 Insertion GC
Two nucleotides GC were inserted after the G at coordinate 877622 in what had previously been annotated as the intergenic region between YOR298C-A and YOR299W. This region is now part of YOR298C-A, as the start for this ORF was moved 279 bp upstream from 877403 to 877682 (note that YOR298C-A is encoded on the Crick strand). As a result, YOR298C-Ap was increased from 58 aa to 151 aa. See Brachat et al. 2003 and GenBank AY260886. This change was also predicted by Kellis et al. and Cliften et al. 
Query:    361 AATTTGGCCTTGAGATCTGGCAACGTTGGCCCTTGGGCCAGAACCACCAGCTCTTGCTCT 420              
              ||||||||||||||||||||||||||||||||||||  ||||||||||||||||||||||
Sbjct: 877587 AATTTGGCCTTGAGATCTGGCAACGTTGGCCCTTGG--CAGAACCACCAGCTCTTGCTCT 877644

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
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

2003-01-09 YOR087W, YOR088W 488439 488439 Insertion T
Due to the insertion of a T after the A at 488439 on chromosome 15, YOR087W and YOR088W have been merged to one single ORF - YVC1/YOR087W, with YOR088W as an alias. The old chromosomal coordinates for YOR087W were 487708-488451, and for YOR088W were 488286-489734. The new chromosomal coordinates for the fused ORF are 487708-489735. The old relative coordinates for YOR087W were 1-744, and for YOR088W were 1-1449. The new relative coordinates for the fused ORF are 1-2028.

Denis V and Cyert MS (2002) Internal Ca(2+) release in yeast is triggered by hypertonic shock and mediated by a TRP channel homologue. J Cell Biol 156(1):29-34.
SGD paper | PubMed | Full-Text
Palmer CP, et al. (2001) A TRP homolog in Saccharomyces cerevisiae forms an intracellular Ca(2+)-permeable channel in the yeast vacuolar membrane. Proc Natl Acad Sci U S A 98(14):7801-5.
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

2001-05-31 YOR068C, YOR069W 453804 453804 Insertion G
Inserted one G nucleotide after the G at chromosomal coordinate 453805, in the intergenic region to the left of overlapping ORFs YOR068C and YOR068W: 
Old: 453752 ATCCTGCAATAACAAGCCATGGACTACGAGGATAATCTAGAAGCACCTGTTTGG-ACGAA 453810
            |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
New: 453752 ATCCTGCAATAACAAGCCATGGACTACGAGGATAATCTAGAAGCACCTGTTTGGGACGAA 453811
1997-08-11 YOL025W 276609 276609 Substitution G A
A single nucleotide substitution was made in the systematic sequence in the region covering the ORF LAG2/YOL025W. The G at 276609 was changed to an A. 
New: 276601 AAAGCAGGAAATTTTACCCAAAAAATTGATGAAGGAGTGACCTTAAGAACAATGATTCTT 276660
            |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Old: 276601 AAAGCAGGGAATTTTACCCAAAAAATTGATGAAGGAGTGACCTTAAGAACAATGATTCTT 276660



Annotation Changes without sequence changes

Date Affected Features
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