Difference between revisions of "Chromosome V History"

From SGD-Wiki
Jump to: navigation, search
(Sequence Changes)
Line 287: Line 287:
 
'''Wang X, et al.''' (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85. <br>
 
'''Wang X, et al.''' (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85. <br>
 
[https://www.yeastgenome.org/reference/S000051920 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8816449 PubMed] | [https://mcb.asm.org/content/16/10/5375 Full-Text] <br>
 
[https://www.yeastgenome.org/reference/S000051920 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/8816449 PubMed] | [https://mcb.asm.org/content/16/10/5375 Full-Text] <br>
 +
 +
|}
 +
 +
<br><br>
 +
 +
=Annotation Changes ''without sequence changes''=
 +
{| border="1" style="border-collapse:collapse; width:90%" cellpadding="6"
 +
! Date  !! Affected Features
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS507 ARS507], [https://www.yeastgenome.org/locus/ARS508 ARS508], [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS512 ARS512], [https://www.yeastgenome.org/locus/ARS513.7 ARS513.7], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS516 ARS516], [https://www.yeastgenome.org/locus/ARS518 ARS518], [https://www.yeastgenome.org/locus/ARS520 ARS520], [https://www.yeastgenome.org/locus/ARS523 ARS523] <br>
 +
As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome V based on Liachko et al. 2013: ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS503 ARS503], [https://www.yeastgenome.org/locus/ARS507 ARS507], [https://www.yeastgenome.org/locus/ARS510 ARS510],  [https://www.yeastgenome.org/locus/ARS511 ARS511], [https://www.yeastgenome.org/locus/ARS514 ARS514], [https://www.yeastgenome.org/locus/ARS516 ARS516],  [https://www.yeastgenome.org/locus/ARS520 ARS520], [https://www.yeastgenome.org/locus/ARS523 ARS523] <br>
 +
The chromosomal coordinates of the following ARS elements on Chromosome V were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-19
 +
| [https://www.yeastgenome.org/locus/ARS513.5 ARS513.5], [https://www.yeastgenome.org/locus/ARS513.7 ARS513.7] <br>
 +
The following new ARS elements on Chromosome V were added to the genome annotation based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS513.5, ARS513.7. <br> <br>
 +
'''Liachko I, et al.''' (2013) High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res 23(4):698-704. <br>
 +
[https://www.yeastgenome.org/reference/S000152760 SGD paper] | [https://www.ncbi.nlm.nih.gov/pubmed/23241746 PubMed] | [https://genome.cshlp.org/content/23/4/698 Full-Text]
 +
|-
 +
| 2014-11-18
 +
| [https://www.yeastgenome.org/locus/YER109C YER109C] <br>
 +
The feature_type annotation of FLO8/YER109C was changed from ORF to blocked_reading_frame (SO:0000718) as part of SGD's genome annotation revision R64.2. <br> <br>

Revision as of 11:54, 4 October 2019

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

  • The sequence of Chromosome V has been updated 20 times, affecting 19 features.
  • The annotation of Chromosome V has been updated 41 times, affecting 92 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 YER075C 308627 308627 Substitution C G
308984 308984 Substitution G T
309047 309047 Substitution G C
Nucleotide substitutions within the coding region of PTP3/YER075C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 717 is now Alanine rather than Proline, and residue 738 is now Lysine rather than Q, and residue 857 is now Glutamine rather than Glutamic Acid.
New   308581  GTCATAAATGAAAATAAATTGATTAATGTTCTGGACCATGGATATTCGTTGCTTTCTAAA  308640
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Old   308577  GTCATAAATGAAAATAAATTGATTAATGTTCTGGACCATGGATATTCGTTCCTTTCTAAA  308636

New   308941  TAACAATTCATAAGGTTTCTCTTGATCATGATATGTTAGCAGAATTTTTCTTATGAGAAT  309000
              ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old   308937  TAACAATTCATAAGGTTTCTCTTGATCATGATATGTTAGCAGAATTTGTCTTATGAGAAT  308996
New   309001  TGCGTCATCATCATCATCATCATCATCATCACAAGCAGCAGCAGTAACAGCAATATTACT  309060
              |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Old   308997  TGCGTCATCATCATCATCATCATCATCATCACAAGCAGCAGCAGTAACAGGAATATTACT  309056

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 YER162C 502222 502222 Substitution T A
A single nucleotide substitution within the coding region of RAD4/YER162C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 223 is now Valine rather than Glutamic Acid.
New   502201  CTTTCCAGGTTCTCATATAAAGTCCCACATTATCATATTTTTTAGTGATCTTCCAGTGTT  502260
              |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Old   502196  CTTTCCAGGTTCTCATATAAAGTCCCTCATTATCATATTTTTTAGTGATCTTCCAGTGTT  502255

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 YER041W 232634 232634 Substitution C G
A single nucleotide substitution within the coding region of YEN1/YER041W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 59 is now Alanine rather than Proline.
New   232621  ATATAGATATAAGCGCCAGATCTAGATCAAGATCAAGGAGTCCTACCCGTTCTCCGCGTG  232680
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old   232620  ATATAGATATAAGCCCCAGATCTAGATCAAGATCAAGGAGTCCTACCCGTTCTCCGCGTG  232679

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 YER061C 278525 278526 Substitution CG GC
Nucleotide changes within the coding region of CEM1/YER061C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 367 is now Alanine rather than Arginine.
New   278521  GCGCCAGCTGCACCTAAAAGATGGCCAATTGCACCTTTGTTACTGGATATGTACAGTGGC  278580
              ||||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||
Old   278519  GCGCCACGTGCACCTAAAAGATGGCCAATTGCACCTTTGTTACTGGATATGTACAGTGGC  278578

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 YER073W 305258 305258 Substitution G A
A single nucleotide substitution within the coding region of ALD5/YER073W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 411 is now Glutamic Acid rather than Glycine.
New   305221  GGTTATTTTGTCAAGCCAACAGTGTTTGCTGATGTCAAAGAAGATATGAGAATTGTTAAG  305280
              |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Old   305218  GGTTATTTTGTCAAGCCAACAGTGTTTGCTGATGTCAAAGGAGATATGAGAATTGTTAAG  305277

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 YEL007W, YEL008W 141112 141112 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs YEL008W and YEL007W.
 New    141061  GCAATGATCTGTCCAACTCACCGAAACAAGAAAAAATTTTGCGTTTTTTTTTTCCTACAAATCCCCCATT  141130
               |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Old    141061  GCAATGATCTGTCCAACTCACCGAAACAAGAAAAAATTTTGCGTTTTTTTTT-CCTACAAATCCCCCATT  141129

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 YEL070W, YEL071W 18079 18079 Substitution A T
A single nucleotide substitution was made in the intergenic region between ORFs DLD3/YEL071W and DSF1/YEL070W.
New    18061   ATCTCCTGATTGCGTACTTCAAAAAGTGTTCGTCCATTTTTTCTTTACTACATTAGATAA  18120
               |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Old    18061   ATCTCCTGATTGCGTACTACAAAAAGTGTTCGTCCATTTTTTCTTTACTACATTAGATAA  18120

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 YER056C, YER056C-A 268857 268857 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs FCY2/YER056C and RPL34A/YER056C-A.
New    268801  AACTTGGTTGAAAGTGGCTGAATTTACGACGTAATCTGTCTTGACATCTTTTTTTTTTTCAGCGAGCATT  268870
               |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Old    268800  AACTTGGTTGAAAGTGGCTGAATTTACGACGTAATCTGTCTTGACATCTTTTTTTTTT-CAGCGAGCATT  268868

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 YER072W, YER073W 303532 303532 Insertion T
A single nucleotide insertion was made in the intergenic region between ORFs VTC1/YER072W and ALD5/YER073W.
New    303481  CCGTTTACACATCAATGATAAATAAGTATACAAAAAGGGTTCCATTTTTTTTTTTGGCCGCTACCGGACT  303550
               |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old    303479  CCGTTTACACATCAATGATAAATAAGTATACAAAAAGGGTTCCATTTTTTTTTT-GGCCGCTACCGGACT  303547

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 YER133W, tH(GUG)E2 434284 434284 Substitution C T
A single nucleotide substitution was made in the intergenic region between GLC7/YER133W and tH(GUG)E2.
New    434281  CAATTTTTCTTTATTTTCTTTTATTACTATTATCATTACTATTATTATTAGTATTATTAT  434340
               ||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    434277  CAATTTTCCTTTATTTTCTTTTATTACTATTATCATTACTATTATTATTAGTATTATTAT  434336

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 YER138W-A, YER139C 449959 449959 Insertion A
A single nucleotide insertion was made in the intergenic region between ORFs YER138W-A and RTR1/YER139C.
New    449941  GTGGGTTTCCTATGTTCTCGAAGAGAGCTTCAAGTGTATTCTATAAACTAAGAATATTAG  450000
               ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Old    449937  GTGGGTTTCCTATGTTCTCGAAG-GAGCTTCAAGTGTATTCTATAAACTAAGAATATTAG  449995

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 YER073W, ER074W 305968 305968 Substitution T A
305885 305886 Substitution CA TC
305880 305880 Substitution T G
305828 305828 Substitution A G
305710 305710 Insertion A
A single nucleotide insertion and several different substitutions were made in the intergenic region between ORFs ALD5/YER073W and RPS24A/YER074W.
New    305701  CAAAAAAAAAAAAACAAAACAAAAAAATAATAACGTGATAAACATTAATGAACAATGTAT  305760
               ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Old    305698  CAAAAAAAAAAAA-CAAAACAAAAAAATAATAACGTGATAAACATTAATGAACAATGTAT  305756
New    305821  TATTGTATATTGAAATATATAGTAATCAAATTCGTTTCATTGATCAAATTGCTCACTAGT  305880
               ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Old    305817  TATTGTATATTAAAATATATAGTAATCAAATTCGTTTCATTGATCAAATTGCTCACTAGT  305876
New    305881  TCTGTTTTTCAAAATTTCATCTTTATAGGTAGATACAAGTGCCAGAGAGATATATAAACA  305940
               ||| ||||  ||||||||||||||||||||||||||||||||||||||||||||||||||
Old    305877  TCTTTTTTCAAAAATTTCATCTTTATAGGTAGATACAAGTGCCAGAGAGATATATAAACA  305936
New    305941  GAAAACTCTATCGATGTGATAATGTATGCCAATATCGGGACTGTACACCCACACATTTAC  306000
               ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Old    305937  GAAAACTCTATCGATGTGATAATGTATGCCATTATCGGGACTGTACACCCACACATTTAC  305996

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 ARS504 9168 9168 Substitution G T
A single nucleotide substitution was made within ARS504.
New    9121    GTTGGCCTGCCATACTTTAATTGAATAAAAGCTCCGTATATGCTTCTTAAAAATAAGCAA  9180
               ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Old    9121    GTTGGCCTGCCATACTTTAATTGAATAAAAGCTCCGTATATGCTTCTGAAAAATAAGCAA  9180

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

2000-03-16 YER123W 406383 406383 Deletion G
A single G nucleotide was deleted within ORF YER123W at chromosomal coordinate 406383, creating a new stop codon; this ORF is shortened, but a prenylation site is created.
Old: 406381 TGGATAAAGCGATTTTTATACTTTTCTCTTTTTCCTTTTTTTTTTTGATTGGCTGTTTCC 406440
            || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
New: 406381 TG-ATAAAGCGATTTTTATACTTTTCTCTTTTTCCTTTTTTTTTTTGATTGGCTGTTTCC 406439

Wang X, et al. (1996) Prenylated isoforms of yeast casein kinase I, including the novel Yck3p, suppress the gcs1 blockage of cell proliferation from stationary phase. Mol Cell Biol 16(10):5375-85.
SGD paper | PubMed | Full-Text



Annotation Changes without sequence changes

Date Affected Features
2014-11-19 ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523

As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome V based on Liachko et al. 2013: ARS507, ARS508, ARS511, ARS512, ARS513.7, ARS514, ARS516, ARS518, ARS520, ARS523.

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 ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523

The chromosomal coordinates of the following ARS elements on Chromosome V were updated based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS503, ARS507, ARS510, ARS511, ARS514, ARS516, ARS520, ARS523.

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 ARS513.5, ARS513.7

The following new ARS elements on Chromosome V were added to the genome annotation based on Liachko et al. 2013 as part of SGD's genome annotation revision R64.2: ARS513.5, ARS513.7.

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

2014-11-18 YER109C

The feature_type annotation of FLO8/YER109C was changed from ORF to blocked_reading_frame (SO:0000718) as part of SGD's genome annotation revision R64.2.