Difference between revisions of "Chromosome XIII History"

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(Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome XIII systematic reference sequence since its intial release on 1996-07-31. <br> *The...")
 
(→‎Sequence Changes)
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'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YMR262W YMR262W]
 +
| 794225
 +
| 794225
 +
| Substitution
 +
| G
 +
| C
 +
|-
 +
| || colspan="6" | Nucleotide change(s) in the coding region of YMR262W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 167 is now Cysteine rather than Tryptophan.
 +
<pre>New    794220  ATTTTGCCGACTGGCAAGGCACACAAGCAAGCCCATCTCTATACACGATGTAAAGTGCCA  794279
 +
              |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
 +
Old    794219  ATTTTGGCGACTGGCAAGGCACACAAGCAAGCCCATCTCTATACACGATGTAAAGTGCCA  794278</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YMR008C YMR008C], [https://www.yeastgenome.org/locus/YMR009W YMR009W]
 +
| 283468
 +
| 283468
 +
| Insertion
 +
|
 +
| G
 +
|-
 +
| || colspan="6" | A single nucleotide was inserted in the intergenic region between ORFs PLB1/YMR008C and ADI1/YMR009W.
 +
<pre>New    283440  GAAATATCGGAGTCTTGCTATTGTTCAGGGCTTTGCCGGTGCGTAAATAATAGGCTGAAG  283499
 +
              ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
 +
Old    283440  GAAATATCGGAGTCTTGCTATTGTTCAGG-CTTTGCCGGTGCGTAAATAATAGGCTGAAG  283498</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YML131W YML131W], [https://www.yeastgenome.org/locus/YML132W YML132W]
 +
| 9542
 +
| 9542
 +
| Deletion
 +
| T
 +
|
 +
|-
 +
| || colspan="6" | A single nucleotide was deleted from the intergenic region between ORFs COS3/YML132W and YML131W.
 +
<pre>New    9531    TTTTTTTTTTT-GCCTTCTTCATACTTTTACTCCTGCTTTTATTACTCTAAATTTCATTTTTATTTATTC  9599
 +
              ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 +
Old    9531    TTTTTTTTTTTTGCCTTCTTCATACTTTTACTCCTGCTTTTATTACTCTAAATTTCATTTTTATTTATTC  9600</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YMRCtau3 YMRCtau3], [https://www.yeastgenome.org/locus/YMRWdelta20 YMRWdelta20]
 +
| 808976
 +
| 808976
 +
| Substitution
 +
| A
 +
| T
 +
|-
 +
| || colspan="6" | A single nucleotide substitution was made in the intergenic region between LTRs YMRCtau3 and YMRWdelta20.
 +
<pre>New    808920  TGATTTGCGCAACGCAGATACAGATTTTACTTTATTCTTCGTGCCTAAAATGGACCATCGTTTCACTTAC  808989
 +
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
 +
Old    808919  TGATTTGCGCAACGCAGATACAGATTTTACTTTATTCTTCGTGCCTAAAATGGACCAACGTTTCACTTAC  808988</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YML121W YML121W], [https://www.yeastgenome.org/locus/YML122C YML122C]
 +
| 26602
 +
| 26602
 +
| Insertion
 +
|
 +
| T
 +
|-
 +
| || colspan="6" | A single nucleotide was inserted in the intergenic region between ORFs YML122C and GTR1/YML121W.
 +
<pre>New    26580  TTTTATTGAATCTTTTTTTTTTTGTAAGAAAATTAAGGTTTATTAGGCAGAGTATACCGA  26639
 +
              |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
 +
Old    26581  TTTTATTGAATCTTTTTTTTTT-GTAAGAAAATTAAGGTTTATTAGGCAGAGTATACCGA  26639</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2011-02-03
 +
| [https://www.yeastgenome.org/locus/YMR315W-A YMR315W-A], [https://www.yeastgenome.org/locus/YMR316W YMR316W]
 +
| 904639
 +
| 904639
 +
| Insertion
 +
|
 +
| G
 +
|-
 +
| || colspan="6" | A single nucleotide was inserted in the intergenic region between ORFs YMR315W-A and DIA1/YMR316W.
 +
<pre>New    904620  TTCTTTTTTTTGGCGCAGCAAGGGACAATGGTCCCTTTTTGAGAAAATGTTGTAGGCTTG  904679
 +
              ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
 +
Old    904619  TTCTTTTTTTTGGCGCAGCAA-GGACAATGGTCCCTTTTTGAGAAAATGTTGTAGGCTTG  904677</pre>
 +
'''Engel SR, et al.''' (2014) The Reference Genome Sequence of ''Saccharomyces cerevisiae'': Then and Now. G3 (Bethesda) Mar 20;4(3):389-98. <br>
 +
[http://www.yeastgenome.org/reference/24374639/overview SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/24374639 PubMed] | [http://g3journal.org/content/4/3/389 Full-Text]
 +
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 2004-02-28
 +
| [https://www.yeastgenome.org/locus/YMR268W-A YMR268W-A], [https://www.yeastgenome.org/locus/YMR269W YMR269W]
 +
| 804684
 +
| 804684
 +
| Deletion
 +
| C
 +
|
 +
|-
 +
| || colspan="6" | Deleted C at 804684 and moved YMR269W start 208 bp upstream from 804663 (old YMR269W start) to 804455 (YMR268W-A start) based on Brachat et al. 2003. This resulted in the merge of YMR268W-A, which was added in June 2003 based on Kessler et al. 2003, into YMR269W. As a result of this sequence correction and locus merge, the YMR269W protein increases in size from 142 amino acids to 211 amino acids, and YMR268W-A is no longer considered a separate ORF.
 +
<pre>New:    181 AACCTGGATGTAAGCACTGATTCGAATAATGGCAGTATTAAATTTACTC-AAAATGAGGC 239
 +
            ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
 +
Old: 804635 AACCTGGATGTAAGCACTGATTCGAATAATGGCAGTATTAAATTTACTCCAAAATGAGGC 804694</pre>
 +
'''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>
 +
'''Kessler MM, et al.''' (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71. <br>
 +
[https://www.yeastgenome.org/reference/S000073671 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/12566404 PubMed] | [https://genome.cshlp.org/content/13/2/264.long Full-Text] <br>

Revision as of 10:15, 2 October 2019

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

  • The sequence of Chromosome XIII has been updated 13 times, affecting 16 features.
  • The annotation of Chromosome XIII has been updated 32 times, affecting 70 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 YMR290W-A 851740 851740 Substitution G A
851734 851734 Substitution G A
Nucleotide change(s) in the coding region of YMR290W-A resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 105-107 are now KKK rather than RKR. 
New    851700  TAAAGCTAATATTGAAAAAAAAAAAAAAAAAAAAAAGAAAAAGCAAATAAAAAATTTTCA  851759
               ||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||
Old    851699  TAAAGCTAATATTGAAAAAAAAAAAAAAAAAAAAAGGAAAAGGCAAATAAAAAATTTTCA  851758

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 YMR299C 864682 864682 Substitution G T
Nucleotide change(s) in the coding region of DYN3/YMR299C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 223 is now Lysine rather than Threonine. 
New    864660  TCGGTATTAATATCTCACTGCGTTTGACCATTTCAATATGATCTTTCATATCTCTATCTT  864719
               ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Old    864659  TCGGTATTAATATCTCACTGCGTGTGACCATTTCAATATGATCTTTCATATCTCTATCTT  864718

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 YMR317W 908172 908183 Substitution TCAGTGAGTTCG GTAATTAGTTCA
908194 908201 Substitution CGTCAACA GGGCAACG
908216 125495 908216 T C
Nucleotide change(s) in the coding region of YMR317W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 271-279 are now VISSEASWA rather than SVSSEASSS. 
New    908160  CGGCAACGTCTAGCGTAATTAGTTCAGAAGCTTCATGGGCAACGTCTAGCTCAGTGAGCTCGGAAGCTCC  908229
               ||||||||||||||  | | ||||| |||||||||| | |||| |||||||||||||| |||||||||||
Old    908158  CGGCAACGTCTAGCTCAGTGAGTTCGGAAGCTTCATCGTCAACATCTAGCTCAGTGAGTTCGGAAGCTCC  908227

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 YMR262W 794225 794225 Substitution G C
Nucleotide change(s) in the coding region of YMR262W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 167 is now Cysteine rather than Tryptophan. 
New    794220  ATTTTGCCGACTGGCAAGGCACACAAGCAAGCCCATCTCTATACACGATGTAAAGTGCCA  794279
               |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    794219  ATTTTGGCGACTGGCAAGGCACACAAGCAAGCCCATCTCTATACACGATGTAAAGTGCCA  794278

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 YMR008C, YMR009W 283468 283468 Insertion G
A single nucleotide was inserted in the intergenic region between ORFs PLB1/YMR008C and ADI1/YMR009W. 
New    283440  GAAATATCGGAGTCTTGCTATTGTTCAGGGCTTTGCCGGTGCGTAAATAATAGGCTGAAG  283499
               ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old    283440  GAAATATCGGAGTCTTGCTATTGTTCAGG-CTTTGCCGGTGCGTAAATAATAGGCTGAAG  283498

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 YML131W, YML132W 9542 9542 Deletion T
A single nucleotide was deleted from the intergenic region between ORFs COS3/YML132W and YML131W. 
New    9531    TTTTTTTTTTT-GCCTTCTTCATACTTTTACTCCTGCTTTTATTACTCTAAATTTCATTTTTATTTATTC  9599
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    9531    TTTTTTTTTTTTGCCTTCTTCATACTTTTACTCCTGCTTTTATTACTCTAAATTTCATTTTTATTTATTC  9600

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 YMRCtau3, YMRWdelta20 808976 808976 Substitution A T
A single nucleotide substitution was made in the intergenic region between LTRs YMRCtau3 and YMRWdelta20. 
New    808920  TGATTTGCGCAACGCAGATACAGATTTTACTTTATTCTTCGTGCCTAAAATGGACCATCGTTTCACTTAC  808989
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old    808919  TGATTTGCGCAACGCAGATACAGATTTTACTTTATTCTTCGTGCCTAAAATGGACCAACGTTTCACTTAC  808988

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 YML121W, YML122C 26602 26602 Insertion T
A single nucleotide was inserted in the intergenic region between ORFs YML122C and GTR1/YML121W. 
New    26580   TTTTATTGAATCTTTTTTTTTTTGTAAGAAAATTAAGGTTTATTAGGCAGAGTATACCGA  26639
               |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Old    26581   TTTTATTGAATCTTTTTTTTTT-GTAAGAAAATTAAGGTTTATTAGGCAGAGTATACCGA  26639

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 YMR315W-A, YMR316W 904639 904639 Insertion G
A single nucleotide was inserted in the intergenic region between ORFs YMR315W-A and DIA1/YMR316W. 
New    904620  TTCTTTTTTTTGGCGCAGCAAGGGACAATGGTCCCTTTTTGAGAAAATGTTGTAGGCTTG  904679
               ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Old    904619  TTCTTTTTTTTGGCGCAGCAA-GGACAATGGTCCCTTTTTGAGAAAATGTTGTAGGCTTG  904677

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

2004-02-28 YMR268W-A, YMR269W 804684 804684 Deletion C
Deleted C at 804684 and moved YMR269W start 208 bp upstream from 804663 (old YMR269W start) to 804455 (YMR268W-A start) based on Brachat et al. 2003. This resulted in the merge of YMR268W-A, which was added in June 2003 based on Kessler et al. 2003, into YMR269W. As a result of this sequence correction and locus merge, the YMR269W protein increases in size from 142 amino acids to 211 amino acids, and YMR268W-A is no longer considered a separate ORF. 
New:    181 AACCTGGATGTAAGCACTGATTCGAATAATGGCAGTATTAAATTTACTC-AAAATGAGGC 239
            ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| 
Old: 804635 AACCTGGATGTAAGCACTGATTCGAATAATGGCAGTATTAAATTTACTCCAAAATGAGGC 804694

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
Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71.
SGD paper | PubMed | Full-Text

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