Details of 2021 Reference Genome Annotation Update R64.3

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.

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
• 2 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C
• 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

Chr	Feature	Description of change	Reference
II	YNCB0008W aka GAL10-ncRNA	New ncRNA antisense to GAL10 coordinates 276805..280645	Houseley et al 2008 PMID:19061643, Pinskaya et al 2009 PMID:19407817, Geisler et al 2012 PMID:22226051
II	YNCB0014W aka TBRT/XUT_2F-154	New ncRNA antisense to TAT1 coordinates 376610..378633	Awasthi et al 2020 PMID:32081726
III	RE/RE301	New recombination enhancer coordinates 29108..29809	Wu and Haber 1996 PMID:8861911
V	YELWdelta27	New Ty1 LTR coordinates 449274..449626	Nene et al 2018 PMID:29320491
V	HPA3/YEL066W	Moved translation start to Met19 old coordinates: 26667..27206 new coordinates: 26721..27206	Sampath et al 2013 PMID:23775086
VII	OTO1/YGR227C-A	New ORF coordinates 949052..949225 Crick	Makanae et al 2015 PMID:25781884
VII	ROK1/YGL171W	Two new uORFs coordinates uORF1: 182286..182407 coordinates uORF2: 182291..182329	Jeon and Kim 2010 PMID:20969870
VIII	YHR052C-B	New ORF coordinates: 212519..212692 Crick	He et al 2018 PMID:29897761
VIII	YHR054C-B	New ORF coordinates: 214517..214690 Crick	He et al 2018 PMID:29897761
VIII	SUT169/YNCH0011W	New ncRNA coordinates 378254..379237	Xu et al 2009 PMID:19169243, Geisler et al 2012 PMID:22226051, Huber et al 2016 PMID:27292640, Bunina et al 2017 PMID:28977638
X	YJR012C	Moved start to Met76 old coordinates: 459795..460418 Crick new coordinates: 459795..460193 Crick	Sadhu et al 2018 PMID:29632376
X	YJR107C-A	New ORF coordinates 628457..628693 Crick	Yagoub et al 2015 PMID:26554900, He et al 2018 PMID:29897761
XI	YKL104W-A	New ORF coordinates 245032..245286	He et al 2018 PMID:29897761
XII	YLR379W-A	New ORF coordinates: 877444..877716	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 old coordinates 559199..559870 new coordinates 559199..559780, 560156..560812	Eisenberg-Bord et al 2018 PMID:29187527
XIII	https://www.yeastgenome.org/locus/S000303813 YMR008C-A]	New ORF coordinates 283081..283548 Crick	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 coordinates: 23564..26578	Camblong et al 2007 PMID:18022365
XIV	LTO1/YNL260C	Move start to Met37 old coordinates: 156859..157455 Crick new coordinates: 156859..157347 Crick	Paul et al 2015 PMID:26182403
XVI	YNCP0002W aka GAL4 lncRNA	New ncRNA coordinates: 79562..82648	Geisler et al 2012 PMID:22226051