Difference between revisions of "Chromosome VIII History"

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(Annotation Changes without sequence changes)
(Annotation Changes without sequence changes)
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'''Nieduszynski CA, et al.''' (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. <br>
 
'''Nieduszynski CA, et al.''' (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9. <br>
 
[https://www.yeastgenome.org/reference/S000117321 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/16847347 PubMed] | [http://genesdev.cshlp.org/content/20/14/1874.long Full-Text] | [http://genesdev.cshlp.org/content/20/14/1874/suppl/DC1 Web Supplement]<br>
 
[https://www.yeastgenome.org/reference/S000117321 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/16847347 PubMed] | [http://genesdev.cshlp.org/content/20/14/1874.long Full-Text] | [http://genesdev.cshlp.org/content/20/14/1874/suppl/DC1 Web Supplement]<br>
 +
|-
 +
| 2006-04-13
 +
| [https://www.yeastgenome.org/locus/ARS808 ARS808]<br>
 +
ARS808, also known as ARS2, was added to the genome annotation for Chromosome VII at coordinates 140342-141267 based on Wyrick et al. 2001 and Hsiao & Carbon 1981. "ARS2" is being retained as the Standard Gene Name for historical reasons, but the systematic name "ARS808" is being used for consistency purposes, to indicate that this ARS is part of Chromosome VIII.<br> <br>
 +
'''Hsiao CL and Carbon J''' (1981) Characterization of a yeast replication origin (ars2) and construction of stable minichromosomes containing cloned yeast centromere DNA (CEN3). Gene 15(2-3):157-66. <br>
 +
[https://www.yeastgenome.org/reference/S000041563 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/7028571 PubMed] | [https://www.sciencedirect.com/science/article/pii/0378111981901256?via%3Dihub Full-Text]<br>
 +
'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>
 +
[https://www.yeastgenome.org/reference/S000069019 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] | [https://science.sciencemag.org/content/294/5550/2357.long Full-Text] | [https://www.ncbi.nlm.nih.gov/pubmed/11743187 Comments & Errata]<br>
 +
|-
 +
| 2006-04-13
 +
| [https://www.yeastgenome.org/locus/ARS805 ARS805]<br>
 +
ARS805, also known as "SPO11 ARS", was added to the genome annotation for Chromosome VIII at coordinates 64155-64459 based on Wyrick et al. 2001 and Atcheson et al. 1987.<br> <br>
 +
'''Atcheson CL, et al.''' (1987) Isolation, DNA sequence, and regulation of a meiosis-specific eukaryotic recombination gene. Proc Natl Acad Sci U S A 84(22):8035-9. <br>
 +
[https://www.yeastgenome.org/reference/S000053823 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/3317399 PubMed] | [https://www.sciencedirect.com/science/article/pii/0378111981901256?via%3Dihub Full-Text]<br>
 +
'''Wyrick JJ, et al.''' (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60. <br>
 +
[https://www.yeastgenome.org/reference/S000069019 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/11743203 PubMed] | [https://www.pnas.org/content/84/22/8035.long Full-Text]<br>

Revision as of 12:14, 30 September 2019

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

  • The sequence of Chromosome VII has been updated 33 times, affecting 40 features.
  • The annotation of Chromosome VII has been updated 24 times, affecting 69 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 ARS814, YHR092C 287178 287178 Insertion C
287123 287123 Deletion C
287116 287116 Deletion G
One single nucleotide was inserted, and two single nucleotides deleted, within the ORF HXT4/YHR092C near its 3' end, altering its coding sequence. The start and majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 16 amino acids longer. The two nucleotide deletions also alter the sequence of the overlapping ARS814.
New   287091  CCGAACATCTTCTTGTAAAATGG-TTGATC-ATCATGCATTAGATCATCAGCGTTGTAGT  287148
              ||||||||||||||||||||||| |||||| |||||||||||||||||||||||||||||
Old   287093  CCGAACATCTTCTTGTAAAATGGGTTGATCCATCATGCATTAGATCATCAGCGTTGTAGT  287152

New   287149  CAGTACCTCTCTTGTTTGGTGGAACCCAAGAAGGTGATTTCCATGGCAAAACACCTTCTT  287208
              |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Old   287153  CAGTACCTCTCTTGTTTGGTGGAACC-AAGAAGGTGATTTCCATGGCAAAACACCTTCTT  287211

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 YHR049C-A 207353 207353 Deletion A
A single nucleotide was deleted near the middle of ORF YHR049C-A, altering its coding sequence. The start remains the same, but the C-terminal half of the protein sequence has changed and the annotated protein is now five amino acids shorter.
New 207360 GTGCTGCTAA-CCCCGCCCGGCGCGAAAAATCCACCCGGGGTGCTTTAGCGTGGCTTACGAAGACCTTTT  207418
           |||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old 207353 GTGCTGCTAAACCCCGCCCGGCGCGAAAAATCCACCCGGGGTGCTTTAGCGTGGCTTACGAAGACCTTTT  207412

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 YHR095W 293374 293374 Insertion C
A single C nucleotide was inserted within ORF YHR095W, near its 3' end, altering its coding sequence. The start and majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 20 amino acids longer.
New   293329  TACGTTTTTGCAAGCAAAAATGAAGATAATCCGAGCGCATGCGCAAGTAGTCCCTGCCAT  293388
              ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Old   293332  TACGTTTTTGCAAGCAAAAATGAAGATAATCCGAGCGCATGCG-AAGTAGTCCCTGCCAT  293390

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 YHR168W 441869 441869 Insertion G
A single G nucleotide was inserted very near the 3' end of ORF MTG2/YHR168W, altering its coding sequence. The start and most of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 19 amino acids longer.
New   441827  GTCAGGAATGGGACTGTGTTCCGATAAGCGCCCTCAGAGAGGAAAACATAGATGTGTTAA  441886
              ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Old   441829  GTCAGGAATGGGACTGTGTTCCGATAAGCGCCCTCAGAGAG-AAAACATAGATGTGTTAA  441887

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 YHL037C 441869 441869 Deletion G
A single nucleotide was deleted within the ORF YHL037C, altering its coding sequence. The start and majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 26 amino acids shorter.
New   25801   ATGCAAGGGTTATGG-CATGCGCATCCATGTGGCGTTTCCTACTTTTATTTTTACATAAT  25859
              ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old   25798   ATGCAAGGGTTATGGGCATGCGCATCCATGTGGCGTTTCCTACTTTTATTTTTACATAAT  25857

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 YHL047C 8358 8358 Insertion G
A single nucleotide was inserted within the ORF ARN2/YHL047C near its 3' end, altering its coding sequence. The start and majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 17 amino acids shorter.
New   8341    TAAATCTTTCTTATGACCTGCCTAAGGCCTTTGCAAAACGTTTCGCGATCCAGTCATTGA  8400
              ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Old   8340    TAAATCTTTCTTATGACCT-CCTAAGGCCTTTGCAAAACGTTTCGCGATCCAGTCATTGA  8398

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 YHR056C, YHR056W-A 217753 217753 Substitution G T
A single nucleotide substitution within the coding region of YHR056W-A resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 116 is now Cysteine rather than Glycine. This nucleotide change also altered the DNA sequence, but not the amino acid sequence, of overlapping ORF RSC30/YHR056C.
New   217731  CAATTCCCACATATCGGTTTTGCCCTGTCGCACCCGATCTTTCTCTTCCTGCATTGGGTG  217790
              |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Old   217733  CAATTCCCACATATCGGTTTGGCCCTGTCGCACCCGATCTTTCTCTTCCTGCATTGGGTG  217792

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 YHR072W 240687 240687 Substitution G A
A single nucleotide substitution within the coding region of ERG7/YHR072W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 530 is now Asparagine rather than Aspartic Acid.
New   240651  AATGGAAACCTTGAATCCTGCTGAAGTTTTTGGTAACATAATGGTAGAATACCCATACGT  240710
              |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Old   240653  AATGGAAACCTTGAATCCTGCTGAAGTTTTTGGTGACATAATGGTAGAATACCCATACGT  240712

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 YHR197W 496180 496180 Substitution G A
A single nucleotide substitution within the coding region of RIX1/YHR197W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 762 is now Glutamic Acid rather than Glycine.
New   496127  GTTTGAAATTCCCGCTATCGAATTAAGTGATGACGAAGAGGAGGAGGAAGAAGAAGAATA  496186
              ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Old   496127  GTTTGAAATTCCCGCTATCGAATTAAGTGATGACGAAGAGGAGGAGGAAGAAGGAGAATA  496186

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 YHL040C, YHL041W 18567 18567 Insertion G
A single nucleotide insertion was made in the intergenic region between ORFs YHL041W and ARN1/YHL040C.
New    18541   CTATCTCTTTACAAGCTGAATGGAATGGGGCTTAGCCGACTGGAAGGATAGGCTTGCCAA  18600
               ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old    18539   CTATCTCTTTACAAGCTGAATGGAATGGG-CTTAGCCGACTGGAAGGATAGGCTTGCCAA  18597

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 TEL08L-YP, YHL050C 2251 2251 Insertion C
A single nucleotide insertion was made in the left telomere of chromosome 8, specifically within Y' element TEL08L-YP and the intron of overlapping ORF YHL050C.
New    2221    CTTAATTGGTGGCAATTCACCCTTACGATTCCTTGCGGCCCAACTGTTTTTTCTAGATAA  2280
               ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Old    2221    CTTAATTGGTGGCAATTCACCCTTACGATTC-TTGCGGCCCAACTGTTTTTTCTAGATAA  2279

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 YHR095W, YHR096C 294437 294437 Deletion A
A single nucleotide deletion was made in the intergenic region between ORFs YHR095W and HXT5/YHR096C.
New    294409  ATCCTACTTAAAATAAAGAAAAAAAA-CAAAAACGTCATGATGATTTTGATATTATTAGA  294467
               |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Old    294411  ATCCTACTTAAAATAAAGAAAAAAAAACAAAAACGTCATGATGATTTTGATATTATTAGA  294470

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 YHR009C, YHR010W 126326 126326 Insertion C
A single nucleotide insertion was made in the intergenic region between ORFs YHR009C and RPL27A/YHR010W.
New    126300  GAACTGTCTGAGACAAAGTCTTTCCAGCAGAGCTCCGCCTACGCTCTTGCTGCAGAGATT  126359
               |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Old    126295  GAACTGTCTGAGACAAAGTCTTTCCAGCAGAG-TCCGCCTACGCTCTTGCTGCAGAGATT  126353

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 YHR013C, YHR014W 131454 131454 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs ARD1/YHR013C and SPO13/YHR014W.
New    131450  TGACGAAGTTTTATTTTGGAGCTTGATCGTATGTATTTAGGTTTCCCTTTTCACTTGGCAATTACTCGTT  131519
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    131444  TGACGAAGTTT-ATTTTGGAGCTTGATCGTATGTATTTAGGTTTCCCTTTTCACTTGGCAATTACTCGTT  131512

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 YHL023C, tH(GUG)H 62687 62687 Substitution G A
A single nucleotide substitution was made in the intergenic region between ORF NPR3/YHL023C and tRNA tH(GUG)H.
New    62640   CTATGTTTAATGGTATTTCAAGATATCACAAGCGAAAAAGTTACTTAAGAAAAAAGACTA  62699
               ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Old    62638   CTATGTTTAATGGTATTTCAAGATATCACAAGCGAAAAAGTTACTTAAGGAAAAAGACTA  62697

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 YHL012W, YHL013C 78734 78734 Insertion G
A single nucleotide insertion was made in the intergenic region between ORFs OTU2/YHL013C and YHL012W.
New    78720   ATTAAAAAAAGAATGCAGGAATAGCACCTTATAGTAAAAAAAGTAAATTTAAGTAATTAA  78779
               |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Old    78717   ATTAAAAAAAGAATGCAG-AATAGCACCTTATAGTAAAAAAAGTAAATTTAAGTAATTAA  78775

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 ARS805 64392 64392 Insertion A
A single nucleotide insertion was made within ARS805.
New    64380   AACATTAAAAAAAAAATTGTCACTACACAGAGAGAAAATAAATAAATATAAAGAATCACA  64439
               ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Old    64378   AACATTAAAAAAAAA-TTGTCACTACACAGAGAGAAAATAAATAAATATAAAGAATCACA  64436

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 YHR132C, YHR132W-A 369889 369889 Insertion A
369987 369987 Deletion T
A single nucleotide insertion and a single nucleotide deletion were made in the intergenic region between ORFs ECM14/YHR132C and IGO2/YHR132W-A.
New    369838  GTCTTTTAAACCGTCGAAAATATTTTATCCTTCCTTCCATTTAGTTGGAACCATTTTCTA  369897
               ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Old    369841  GTCTTTTAAACCGTCGAAAATATTTTATCCTTCCTTCCATTTAGTTGGA-CCATTTTCTA  369899
New    369948  TGATCTTTTAAATTACAGGTTATCGCGGGAGAATATT-GGGGTTCAGAAATACAACACAT  370006
               ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Old    369950  TGATCTTTTAAATTACAGGTTATCGCGGGAGAATATTTGGGGTTCAGAAATACAACACAT  370009

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 RUF5-1, YHR052W 212258 212258 Deletion A
212270 212276 Deletion TTTTTTT
A single nucleotide deletion and a heptanucleotide deletion were made in the intergenic region between ORF YHR052W and ncRNA RUF5-1.
New    212229  ACGTTCTCATAATACATTTTAGGATTAATACATAT-GCTTTTTTTTT-------ATTCGAAATCT  212285
               ||||||||||||||||||||||||||||||||||| |||||||||||       |||||||||||
Old    212223  ACGTTCTCATAATACATTTTAGGATTAATACATATAGCTTTTTTTTTTTTTTTTATTCGAAATCT  212287

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 YHR170W, YHR171W 445615 445615 Insertion G
A single nucleotide insertion was made in the intergenic region between NMD3/YHR170W and ATG7/YHR171W.
New    445607  CCGGCACGGCAAAACAAAAAAATTAAGGGAACTCATTATTTTACGATGCTACTTAGATAA  445666
               |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Old    445608  CCGGCACG-CAAAACAAAAAAATTAAGGGAACTCATTATTTTACGATGCTACTTAGATAA  445666

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 YHR162W, YHR163W 423723 423723 Insertion C
A single nucleotide insertion was made in the intergenic region between ORFs YHR162W and SOL3/YHR163W.
New    423707  CCCTGGTCCGCGACCAAATGGTGACAGTCGGTGTGTTTTCTGAGAGGGCTAGTTTGACCC  423766
               |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old    423710  CCCTGGTCCGCGAC-AAATGGTGACAGTCGGTGTGTTTTCTGAGAGGGCTAGTTTGACCC  423768

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 YHL002W, YHL003C 102564 102564 Insertion C
A single nucleotide insertion was made in the intergenic region between ORFs LAG1/YHL003C and HSE1/YHL002W.
New    102540  ATTCTAACTGTTAAATATAGGGGCCATGCCAGAGGCAATGCGTAAATCTATCTAAGGAAA  102599
               ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old    102536  ATTCTAACTGTTAAATATAGGGGCCATGC-AGAGGCAATGCGTAAATCTATCTAAGGAAA  102594

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

2005-11-08 YHL026C 54135 54135 Insertion G
Based on the automated comparison of closely related Saccharomyces species, Cliften et al. suggest that the start site for YHL026C be moved 141 nt upstream. SGD confirmed the insertion of a single G nt between the G at 54135 and the T at 54136. As a consequence of this sequence change, YHL026C will be extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 268 to 315 amino acids.
New:       ATGGAATTTCTGAACCCGGTCGGGGTCGCTGGCGCTGGCTCTGAGGATTTCATATATGTG
           |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Old: 54112 ATGGAATTTCTGAACCCGGTCGGG-TCGCTGGCGCTGGCTCTGAGGATTTCATATATGTG  54170

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

2004-07-26 YHR131C, YHR131W-A 367891 367891 Insertion C
The work of Kellis et al. proposed an insertion that would extend the YHR131C reading frame. This sequence error was confirmed in S288C by SGD. As a consequence of this change, YHR131C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 840 to 850 amino acids. In addition, YHR131W-A was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 115 to 81 amino acids.
New:        TAATTTGCCCTCTATTGGCAGAGCCATCCTTAACAAACGAACAACTTGTATGCACGATGT
            |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Old: 367868 TAATTTGCCCTCTATTGGCAGAGC-ATCCTTAACAAACGAACAACTTGTATGCACGATGT 367926

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

2004-07-26 YHL006C 98461 98461 Insertion C
Kellis et al. predicted and confirmed the insertion of a single C nt. As a consequence of this sequence change, YHL006C was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 159 to 150 amino acids.
New: 98439 GCCGTAACACAAGGCTAAGTAGCCGCAGCTGTTGCGGTCCATCTTGTGTCGCGGTGAGAT 98498
           ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Old: 98439 GCCGTAACACAAGGCTAAGTAGC-GCAGCTGTTGCGGTCCATCTTGTGTCGCGGTGAGAT 98497

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

2004-02-01 YHR176W 455503 455503 Insertion C
455307 455307 Insertion G
Based on the comparison of related fungi, Brachat et al. suggested that the C-terminus of Fmo1p/YHR176Wp be extended at the C-Terminus. Zhang and Robertus resequenced this gene (in 2 S288C derived strains, X2180 and TR2), confirming the insertion of two nucleotides. As a consequence of these sequence changes, FMO1/YHR176W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 373 to 432 amino acids.
New: 455286 GGAACGCACAACTTCCCAAAGGGAAAGGACCTGGAATACTATGCAGAACTACAGGAACTA 455345
            |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Old: 455286 GGAACGCACAACTTCCCAAAGG-AAAGGACCTGGAATACTATGCAGAACTACAGGAACTA 455344

New: 455346 CTGAATAGCATTCCACGTAGGGTCGGTCATTTCGAACCAGTTGTATGGGATGATAGACTG 455405
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old: 455345 CTGAATAGCATTCCACGTAGGGTCGGTCATTTCGAACCAGTTGTATGGGATGATAGACTG 455404

New: 455406 ATCGATCTAAGAAACAGTAGTTATACAGACAAAGAAGAAAGAAATGTGCTTCTAGCGGAA 455465
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old: 455405 ATCGATCTAAGAAACAGTAGTTATACAGACAAAGAAGAAAGAAATGTGCTTCTAGCGGAA 455464

New: 455466 CACGCACAAGCCCTAAAGAAAAAAAAAGCACCATACTTCCTTCCGGCGCCACATACTTAA 455525
            ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Old: 455465 CACGCACAAGCCCTAAAGAAAAAAAAAGCACCATACTTC-TTCCGGCGCCACATACTTAA 455523

Zhang M and Robertus JD (2002) Molecular cloning and characterization of a full-length flavin-dependent monooxygenase from yeast. Arch Biochem Biophys 403(2):277-83.
SGD paper | PubMed | Full-Text
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

2004-07-26 YHR056C, YHR056W-A 217751 217751 Deletion T
Based on the automated comparison of related fungi, Cliften et al. and Brachat et al. both suggest that the start site for RSC30/YHR056C be moved 155 nt upstream. Based on experimental evidence, Angus-Hill et al. proposed the deletion of a single T nt upstream of RSC30/YHR056C, allowing a 51 amino acid N-terminal extension. This sequence change was confirmed in S288c by SGD. As a consequence of this sequence change, two ORFs were extended: (1) RSC30/YHR056C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 832 to 883 amino acids; (2) YHR056W-A was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 143 to 144 amino acids.
New: 217704 AAAACAGTCCGGCTTGTTATACTTGACGCAATTCCCACATATCGGTTT-GGCCCTGTCGC 217762
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Old: 217704 AAAACAGTCCGGCTTGTTATACTTGACGCAATTCCCACATATCGGTTTTGGCCCTGTCGC 217763

Angus-Hill ML, et al. (2001) A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. Mol Cell 7(4):741-51.
SGD paper | PubMed | Full-Text | YFGdb
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

2000-01-21 YHR132W-A 370332 370332 Insertion C
A single C nucleotide was inserted after the C at chromosomal coordinate 370331, resulting in the creation of a new ORF YHR132W-A spanning coordinates 370055-370450. See GenBank files: YSCH9315 GenBank entry, accession U10398, U00093. Thank you to Atsuko Horiuchi for alerting SGD to this omission.
New:  aatcctagcggtttaagagag
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Old:  aatc-tagcggtttaagagag



Annotation Changes without sequence changes

Date Affected Features
2014-11-19 ARS802, ARS805, ARS807, ARS813, ARS818, ARS820

As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome VIII based on Liachko et al. 2013: ARS802, ARS805, ARS807, ARS813, ARS818, ARS820.

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 ARS802, ARS805, ARS807, ARS809, ARS813, ARS815, ARS818, ARS820

The chromosomal coordinates of the following ARS elements on Chromosome VIII were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS802, ARS805, ARS807, ARS809, ARS813, ARS815, ARS818, ARS820.

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

2009-05-06 ARS801, ARS806, ARS810, ARS811, ARS814, ARS815

The following ARS elements on Chromosome 8 were added to the genome annotation based on Raveendranathan et al. 2006: ARS801, ARS806, ARS810, ARS811, ARS814, and ARS815.

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

2007-07-09 YHR076W

An intron was annotated within PTC7/YHR076W at relative coordinates 56..148 based on GenBank EF123135, Juneau et al. 2007, and Zhang et al. 2007. According to Juneau et al. 2007, the intron is "inefficiently spliced" (splicing rate = 55%). Note that the currently annotated start and stop remain the same.

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

2006-09-07 ARS802, ARS807, ARS809, ARS813, ARS818, ARS820, ARS822, ARS824

The following new ARS elements on Chromosome VIII were added to SGD based on Nieduszynski et al. 2006: ARS802, ARS807, ARS809, ARS813, ARS818, ARS820, ARS822, ARS824.

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

2006-09-07 ARS805

The coordinates of ARS805 were updated based on Nieduszynski et al. 2006.

Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9.
SGD paper | PubMed | Full-Text | Web Supplement

2006-04-13 ARS808

ARS808, also known as ARS2, was added to the genome annotation for Chromosome VII at coordinates 140342-141267 based on Wyrick et al. 2001 and Hsiao & Carbon 1981. "ARS2" is being retained as the Standard Gene Name for historical reasons, but the systematic name "ARS808" is being used for consistency purposes, to indicate that this ARS is part of Chromosome VIII.

Hsiao CL and Carbon J (1981) Characterization of a yeast replication origin (ars2) and construction of stable minichromosomes containing cloned yeast centromere DNA (CEN3). Gene 15(2-3):157-66.
SGD paper | PubMed | Full-Text
Wyrick JJ, et al. (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60.
SGD paper | PubMed | Full-Text | Comments & Errata

2006-04-13 ARS805

ARS805, also known as "SPO11 ARS", was added to the genome annotation for Chromosome VIII at coordinates 64155-64459 based on Wyrick et al. 2001 and Atcheson et al. 1987.

Atcheson CL, et al. (1987) Isolation, DNA sequence, and regulation of a meiosis-specific eukaryotic recombination gene. Proc Natl Acad Sci U S A 84(22):8035-9.
SGD paper | PubMed | Full-Text
Wyrick JJ, et al. (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60.
SGD paper | PubMed | Full-Text