Difference between revisions of "Details of 2021 Reference Genome Annotation Update R64.3"
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The ''S. cerevisiae'' strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3.1, dated 2021-04-22. Note that the underlying genome sequence itself was not altered in any way. | The ''S. cerevisiae'' strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3.1, dated 2021-04-22. Note that the underlying genome sequence itself was not altered in any way. | ||
| − | + | ==R64.3 Annotation update summary== | |
This annotation update included (details in table below): | This annotation update included (details in table below): | ||
*7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A] | *7 new ORFs: [https://www.yeastgenome.org/locus/S000303806 OTO1/YGR227C-A], [https://www.yeastgenome.org/locus/S000303807 YHR052C-B], [https://www.yeastgenome.org/locus/S000303808 YHR054C-B], [https://www.yeastgenome.org/locus/S000303810 YJR107C-A], [https://www.yeastgenome.org/locus/S000303811 YKL104W-A], [https://www.yeastgenome.org/locus/S000303812 YLR379W-A], [https://www.yeastgenome.org/locus/S000303813 YMR008C-A] | ||
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*Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2] | *Changed feature_type (and SO_term) for non-transcribed spacers: [https://www.yeastgenome.org/locus/S000029714 NTS1-2], [https://www.yeastgenome.org/locus/S000029329 NTS2-1], [https://www.yeastgenome.org/locus/S000029706 NTS2-2] | ||
*New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs] | *New systematic nomenclature system for [https://www.yeastgenome.org/search?q=YNC&category=locus entire annotated complement of ncRNAs] | ||
| − | + | ==R64.3 Annotation update details== | |
| + | ==New systematic nomenclature system for noncoding RNA genes== | ||
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Revision as of 15:26, 26 April 2021
NOTE: this page still a work in progress
The S. cerevisiae strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3.1, dated 2021-04-22. Note that the underlying genome sequence itself was not altered in any way.
R64.3 Annotation update summary
This annotation update included (details in table below):
- 7 new ORFs: OTO1/YGR227C-A, YHR052C-B, YHR054C-B, YJR107C-A, YKL104W-A, YLR379W-A, YMR008C-A
- 5 new ncRNAs: GAL10-ncRNA, TBRT/XUT_2F-154, SUT169, PHO84 lncRNA, GAL4 lncRNA
- 2 new uORFs for ROK1/YGL171W
- 1 new recombination enhancer: RE
- 1 new LTR: YELWdelta27
- 3 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C, LTO1/YNL260C
- 1 ORF with shifted translation stop plus new intron: LDO45/YMR147W
- Changed feature_type (and SO_term) for non-transcribed spacers: NTS1-2, NTS2-1, NTS2-2
- New systematic nomenclature system for entire annotated complement of ncRNAs
R64.3 Annotation update details
New systematic nomenclature system for noncoding RNA genes
| Chr | Feature | Description of change | Reference |
|---|---|---|---|
| II | YNCB0008W aka GAL10-ncRNA | New ncRNA antisense to GAL10
|
Houseley et al 2008 PMID:19061643,
Pinskaya et al 2009 PMID:19407817,
|
| II | YNCB0014W aka TBRT/XUT_2F-154 | New ncRNA antisense to TAT1
|
Awasthi et al 2020 PMID:32081726 |
| III | RE/RE301 | New recombination enhancer
|
Wu and Haber 1996 PMID:8861911 |
| V | YELWdelta27 | New Ty1 LTR
|
Nene et al 2018 PMID:29320491 |
| V | HPA3/YEL066W | Moved translation start to Met19
|
Sampath et al 2013 PMID:23775086 |
| VII | OTO1/YGR227C-A | New ORF
|
Makanae et al 2015 PMID:25781884 |
| VII | ROK1/YGL171W | Two new uORFs
|
Jeon and Kim 2010 PMID:20969870 |
| VIII | YHR052C-B | New ORF
|
He et al 2018 PMID:29897761 |
| VIII | YHR054C-B | New ORF
|
He et al 2018 PMID:29897761 |
| VIII | SUT169/YNCH0011W | New ncRNA
|
Xu et al 2009 PMID:19169243,
Geisler et al 2012 PMID:22226051,
|
| X | YJR012C | Moved start to Met76
|
Sadhu et al 2018 PMID:29632376 |
| X | YJR107C-A | New ORF
|
Yagoub et al 2015 PMID:26554900, He et al 2018 PMID:29897761 |
| XI | YKL104W-A | New ORF
|
He et al 2018 PMID:29897761 |
| XII | YLR379W-A | New ORF
|
Internal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462 |
| XII | NTS1-2, NTS2-1, NTS2-2 | Change feature_type/SO_term from SO:0001637 rRNA_gene to SO:0000183 non_transcribed_region | |
| XIII | LDO45/YMR147W | Shift stop to be same as LDO16/YMR148W, add intron
|
Eisenberg-Bord et al 2018 PMID:29187527 |
| XIII | YMR008C-A | New ORF
|
Internal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462 |
| XIII | YNCM0001W aka PHO84 lncRNA | New ncRNA
|
Camblong et al 2007 PMID:18022365 |
| XIV | LTO1/YNL260C | Move start to Met37
|
Paul et al 2015 PMID:26182403 |
| XVI | YNCP0002W aka GAL4 lncRNA | New ncRNA
|
Geisler et al 2012 PMID:22226051 |
