Difference between revisions of "Details of 2021 Reference Genome Annotation Update R64.3"

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|New ORF
 
|New ORF
 
*coordinates 628457..628693 Crick
 
*coordinates 628457..628693 Crick
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|PMID:26554900, PMID:29897761
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|[https://www.yeastgenome.org/reference/S000182052 Yagoub et al 2015] PMID:26554900, [https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
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*old coordinates: 459795..460418 Crick
 
*old coordinates: 459795..460418 Crick
 
*new coordinates: 459795..460193 Crick
 
*new coordinates: 459795..460193 Crick
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|PMID:29632376
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|[https://www.yeastgenome.org/reference/S000216555 Sadhu et al 2018] PMID:29632376
 
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*old coordinates 559199..559870
 
*old coordinates 559199..559870
 
*new coordinates 559199..559780, 560156..560812
 
*new coordinates 559199..559780, 560156..560812
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|PMID:29187527
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|[https://www.yeastgenome.org/reference/S000207266 Eisenberg-Bord et al 2018] PMID:29187527
 
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|YNCM0001W aka PHO84 lncRNA
 
|YNCM0001W aka PHO84 lncRNA
 
|New ncRNA
 
|New ncRNA
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*coordinates: 23564..2657
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*coordinates: 23564..26578
 
|[https://www.yeastgenome.org/reference/S000124750 Camblong et al 2007] PMID:18022365
 
|[https://www.yeastgenome.org/reference/S000124750 Camblong et al 2007] PMID:18022365
 
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Revision as of 14:12, 23 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.

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: YELWdetla27
  • 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
 PMID:19169243, PMID:22226051, PMID:27292640, PMID:28977638
X YJR107C-A New ORF
  • coordinates 628457..628693 Crick
 Yagoub et al 2015 PMID:26554900, He et al 2018 PMID:29897761
X YJR012C Moved start to Met76
  • old coordinates: 459795..460418 Crick
  • new coordinates: 459795..460193 Crick
 Sadhu et al 2018 PMID:29632376
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 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
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