Difference between revisions of "Chromosome XI History"

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(Created page with "This page lists all sequence and annotation changes that have been made to the Chromosome XI systematic reference sequence since its intial release on 1996-07-31. <br> *The se...")
 
(Sequence Changes)
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Old    199368  G-ATCTGCAGATGTACAGCCAGCCGCAGCAGTGTAAATATATTGCTCAGGCATTTGCACA  199426</pre>
 
Old    199368  G-ATCTGCAGATGTACAGCCAGCCGCAGCAGTGTAAATATATTGCTCAGGCATTTGCACA  199426</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;"
 +
| rowspan="2"| 2011-02-03
 +
| rowspan="2"| [https://www.yeastgenome.org/locus/YKR012C YKR012C]
 +
| 463468
 +
| 463468
 +
| Substitution
 +
| G
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 463435
 +
| 463435
 +
| Substitution
 +
| G
 +
| T
 +
|-
 +
| || colspan="6" | Nucleotide change(s) in the coding region of YKR012C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 98 is now Lysine rather than Glutamine, and residue 109 is now Lysine rather than Glutamine.
 +
<pre>New    463774  CTCTATATGTAATGTTTTTGAAACATAGACGTCGTTCAAAGGCAATGCTTTTGATCTTTG  463833
 +
              |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||
 +
Old    463417  CTCTATATGTAATGTTTTGGAAACATAGACGTCGTTCAAAGGCAATGCTTTGGATCTTTG  463476</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;"
 +
| rowspan="8"| 2011-02-03
 +
| rowspan="8"| [https://www.yeastgenome.org/locus/YKL134C YKL134C]
 +
| 190415
 +
| 190415
 +
| Insertion
 +
|
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 190409
 +
| 190409
 +
| Insertion
 +
|
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 190408
 +
| 190408
 +
| Insertion
 +
|
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 190405
 +
| 190405
 +
| Insertion
 +
|
 +
| G
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 190404
 +
| 190404
 +
| Insertion
 +
|
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 190397
 +
| 190397
 +
| Insertion
 +
|
 +
| A
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 189367
 +
| 189367
 +
| Insertion
 +
|
 +
| T
 +
|- style="height:30px; width:30px; text-align:center;"
 +
| 189339
 +
| 189339
 +
| Deletion
 +
| A
 +
|
 +
|-
 +
| || colspan="6" | Six single nucleotides were inserted near the middle of ORF OCT1/YKL134C, and one nucleotide was inserted and another deleted near its 3' end, altering the OCT1 coding sequence. The start, stop, and majority of the reading frame remain the same, but the annotated protein is now one amino acid longer and two separate small sections of the protein sequence are now different.
 +
<pre>New    189292  CTCGAAAAGGGCGTACCAGATTTTAGAAGCTATCGTCCTATC-AAATAAGTAGCTGTAAT  189350
 +
              |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
 +
Old    189297  CTCGAAAAGGGCGTACCAGATTTTAGAAGCTATCGTCCTATCAAAATAAGTAGCTGTAAT  189356
 +
New    189351  AAGTTGCCCCGTATCCAAATAAATGGCCGAATCTTCCACACCAATTACTCTGATCGTCCA  189410
 +
              ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
 +
Old    189357  AAGTTGCCCCG-ATCCAAATAAATGGCCGAATCTTCCACACCAATTACTCTGATCGTCCA  189415
 +
New    190371  TTAACGTCAAAATAAAATCTTGAACATCTTTCGGATTCTTTGCCATTTTACCTTCCAATT  190430
 +
              |||||||||||||||||||||| ||||||| | ||| | |||||| ||||||||||||||
 +
Old    190376  TTAACGTCAAAATAAAATCTTG-ACATCTT-C-GAT-C-TTGCCA-TTTACCTTCCAATT  190429</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>
 
'''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]

Revision as of 12:36, 1 October 2019

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

  • The sequence of Chromosome XI has been updated 79 times, affecting 53 features.
  • The annotation of Chromosome XI has been updated 39 times, affecting 55 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 YKL198C 68315 68315 Deletion C
69325 69326 Substitution TG CT
69494 69494 Deletion G
69501 69501 Insertion C
Five nucleotide changes were made within the ORF PTK1/YKL198C, altering its coding sequence: one single insertion, two single deletions, and two substitutions. The start and majority of the reading frame remain the same, but a small section of the annotated protein sequence is now different, the C-terminus has changed, and the annotated protein is now 13 amino acids longer.
New    68277   GACCAAGCTGTTGACAATGTTCAGATGGTGATGCAC-TACCCTGTGCGGGGAGTGGCCAC  68335
               |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Old    68279   GACCAAGCTGTTGACAATGTTCAGATGGTGATGCACCTACCCTGTGCGGGGAGTGGCCAC  68338
New    69296   TACAAAACTTTTCTGCTAGGGCCACGCTGCGCCAGCCCGATTTTTGTATCATCGCGAACA  69355
               ||||||||||||||||||||||||||  ||||||||||||||||||||||||||||||||
Old    69299   TACAAAACTTTTCTGCTAGGGCCACGTGGCGCCAGCCCGATTTTTGTATCATCGCGAACA  69358
New    69476   TGATAAACTCCTTTG-AGCAGCGCTTGTAGAATTTCTCGGGCGTTTCATTATAGATCATA  69534
               ||||||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||
Old    69479   TGATAAACTCCTTTGGAGCAGCG-TTGTAGAATTTCTCGGGCGTTTCATTATAGATCATA  69537

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 YKL157W 158179 158179 Deletion G
A single G nucleotide was deleted within ORF APE2/YKL157W, 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 longer.
New    158153  CTATTACTTCGAAAGCGCAGT-GGGTTAACAGAGACCGTGATGTCGTCAACAAGTATTTG  158211
               ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Old    158158  CTATTACTTCGAAAGCGCAGTGGGGTTAACAGAGACCGTGATGTCGTCAACAAGTATTTG  158217

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 YKR028W 496923 496923 Insertion G
A single G nucleotide was inserted within the ORF SAP190/YKR028W 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 65 amino acids shorter.
New    497254  ATATCAAGCGATGAAGAAGACTCCGAAGATGAAGATGAAGAGAATGATATGGGCAATGAG  497313
               ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||
Old    496897  ATATCAAGCGATGAAGAAGACTCCGAA-ATGAAGATGAAGAGAATGATATGGGCAATGAG  496955

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 YKL129C 197105 197106 Substitution CG GC
199353 199353 Insertion T
199359 199359 Insertion T
199377 199378 Substitution AT TA
199368 199368 Insertion T
Three nucleotides were inserted within the ORF MYO3/YKL129C, and a dinucleotide substitution was also made in the same region, altering the MYO3 coding sequence. A silent dinucleotide substitution was also made within the ORF. The start, stop, and majority of the reading frame remain the same, but the annotated protein sequence is now one amino acid longer and a small section of the sequence has changed.
New    197091  TGTGCAGCGGTAGCTGCCAAAGATAACGGATTCACAGGTTTTTGCGAAGGGAGAGGTTGC  197150
               |||||||||||||||  |||||||||||||||||||||||||||||||||||||||||||
Old    197090  TGTGCAGCGGTAGCTCGCAAAGATAACGGATTCACAGGTTTTTGCGAAGGGAGAGGTTGC  197149
New    199311  ACTAAACCAATGGTTCTCATAGCCTCTAACGTGCCTTCGTAATCTTTTACGTCATCAATT  199370
               |||||||||||||||||||||||||||||||||||||||||||| |||||| ||||||||
Old    199310  ACTAAACCAATGGTTCTCATAGCCTCTAACGTGCCTTCGTAATC-TTTACG-CATCAATT  199367
New    199371  GTATCTGCAGTAGTACAGCCAGCCGCAGCAGTGTAAATATATTGCTCAGGCATTTGCACA  199430
               | ||||||||  ||||||||||||||||||||||||||||||||||||||||||||||||
Old    199368  G-ATCTGCAGATGTACAGCCAGCCGCAGCAGTGTAAATATATTGCTCAGGCATTTGCACA  199426

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 YKR012C 463468 463468 Substitution G T
463435 463435 Substitution G T
Nucleotide change(s) in the coding region of YKR012C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 98 is now Lysine rather than Glutamine, and residue 109 is now Lysine rather than Glutamine.
New    463774  CTCTATATGTAATGTTTTTGAAACATAGACGTCGTTCAAAGGCAATGCTTTTGATCTTTG  463833
               |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||
Old    463417  CTCTATATGTAATGTTTTGGAAACATAGACGTCGTTCAAAGGCAATGCTTTGGATCTTTG  463476

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 YKL134C 190415 190415 Insertion T
190409 190409 Insertion T
190408 190408 Insertion T
190405 190405 Insertion G
190404 190404 Insertion T
190397 190397 Insertion A
189367 189367 Insertion T
189339 189339 Deletion A
Six single nucleotides were inserted near the middle of ORF OCT1/YKL134C, and one nucleotide was inserted and another deleted near its 3' end, altering the OCT1 coding sequence. The start, stop, and majority of the reading frame remain the same, but the annotated protein is now one amino acid longer and two separate small sections of the protein sequence are now different.
New    189292  CTCGAAAAGGGCGTACCAGATTTTAGAAGCTATCGTCCTATC-AAATAAGTAGCTGTAAT  189350
               |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Old    189297  CTCGAAAAGGGCGTACCAGATTTTAGAAGCTATCGTCCTATCAAAATAAGTAGCTGTAAT  189356
New    189351  AAGTTGCCCCGTATCCAAATAAATGGCCGAATCTTCCACACCAATTACTCTGATCGTCCA  189410
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Old    189357  AAGTTGCCCCG-ATCCAAATAAATGGCCGAATCTTCCACACCAATTACTCTGATCGTCCA  189415
New    190371  TTAACGTCAAAATAAAATCTTGAACATCTTTCGGATTCTTTGCCATTTTACCTTCCAATT  190430
               |||||||||||||||||||||| ||||||| | ||| | |||||| ||||||||||||||
Old    190376  TTAACGTCAAAATAAAATCTTG-ACATCTT-C-GAT-C-TTGCCA-TTTACCTTCCAATT  190429

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