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

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Line 71: Line 71:
 
|YHR052C-B
 
|YHR052C-B
 
|New ORF
 
|New ORF
 +
*coordinates: 212519..212692 Crick
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|-
 
|-
Line 76: Line 77:
 
|YHR054C-B
 
|YHR054C-B
 
|New ORF
 
|New ORF
 +
*coordinates: 214517..214690 Crick
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|-
 
|-
Line 81: Line 83:
 
|SUT169/YNCH0011W
 
|SUT169/YNCH0011W
 
|New ncRNA
 
|New ncRNA
 +
*coordinates 378254..379237
 
|PMID:19169243, PMID:22226051, PMID:27292640, PMID:28977638
 
|PMID:19169243, PMID:22226051, PMID:27292640, PMID:28977638
 
|-
 
|-
Line 86: Line 89:
 
|YJR107C-A
 
|YJR107C-A
 
|New ORF
 
|New ORF
 +
*coordinates 628457..628693 Crick
 
|PMID:26554900, PMID:29897761
 
|PMID:26554900, PMID:29897761
 
|-
 
|-
Line 91: Line 95:
 
|YJR012C
 
|YJR012C
 
|Moved start to Met76
 
|Moved start to Met76
−
old coordinates: 459795..460418 Crick
+
*old coordinates: 459795..460418 Crick
−
new coordinates: 459795..460193 Crick
+
*new coordinates: 459795..460193 Crick
 
|PMID:29632376
 
|PMID:29632376
 
|-
 
|-
Line 98: Line 102:
 
|YKL104W-A
 
|YKL104W-A
 
|New ORF
 
|New ORF
 +
*coordinates 245032..245286
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|[https://www.yeastgenome.org/reference/S000217202 He et al 2018] PMID:29897761
 
|-
 
|-
 
|XII
 
|XII
 
|YLR379W-A
 
|YLR379W-A
−
|
+
|New ORF
 +
*coordinates: 877444..877716
 
|
 
|
 
|-
 
|-
Line 113: Line 119:
 
|LDO45/YMR147W
 
|LDO45/YMR147W
 
|Shift stop to be same as LDO16/YMR148W, add intron
 
|Shift stop to be same as LDO16/YMR148W, add intron
−
old coordinates 559199..559870
+
*old coordinates 559199..559870
−
new coordinates 559199..559780, 560156..560812
+
*new coordinates 559199..559780, 560156..560812
 
|PMID:29187527
 
|PMID:29187527
 
|-
 
|-
 
|XIII
 
|XIII
 
|YMR008C-A
 
|YMR008C-A
−
|
+
|New ORF
 +
*coordinates 283081..283548 Crick
 
|
 
|
 
|-
 
|-
Line 125: Line 132:
 
|YNCM0001W aka PHO84 lncRNA
 
|YNCM0001W aka PHO84 lncRNA
 
|New ncRNA
 
|New ncRNA
 +
*coordinates: 23564..2657
 
|PMID:18022365
 
|PMID:18022365
 
|-
 
|-
Line 130: Line 138:
 
|LTO1/YNL260C
 
|LTO1/YNL260C
 
|Move start to Met37
 
|Move start to Met37
−
old coords: 156859..157455 Crick
+
*old coordinates: 156859..157455 Crick
−
new coords: 156859..157347 Crick
+
*new coordinates: 156859..157347 Crick
 
|PMID: 26182403
 
|PMID: 26182403
 
|-
 
|-
Line 137: Line 145:
 
|YNCP0002W aka GAL4 lncRNA
 
|YNCP0002W aka GAL4 lncRNA
 
|New ncRNA
 
|New ncRNA
 +
*coordinates: 79562..82648
 
|PMID: 22226051  
 
|PMID: 22226051  
 
|-
 
|-

Revision as of 09:33, 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):

  • 5 new ncRNAs
  • 1 new recombination enhancer
  • 7 new ORFs
  • 1 new LTR
  • 2 new uORFs
  • 2 ORFs with shifted translation starts
  • 1 ORF with shifted translation stop plus new intron
  • Changed feature_type (and SO_term) for non-transcribed spacers
  • 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
 PMID:26554900, PMID:29897761
X YJR012C Moved start to Met76
  • old coordinates: 459795..460418 Crick
  • new coordinates: 459795..460193 Crick
 PMID:29632376
XI YKL104W-A New ORF
  • coordinates 245032..245286
 He et al 2018 PMID:29897761
XII YLR379W-A New ORF
  • coordinates: 877444..877716
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
 PMID:29187527
XIII YMR008C-A New ORF
  • coordinates 283081..283548 Crick
XIII YNCM0001W aka PHO84 lncRNA New ncRNA
  • coordinates: 23564..2657
 PMID:18022365
XIV LTO1/YNL260C Move start to Met37
  • old coordinates: 156859..157455 Crick
  • new coordinates: 156859..157347 Crick
 PMID: 26182403
XVI YNCP0002W aka GAL4 lncRNA New ncRNA
  • coordinates: 79562..82648
 PMID: 22226051
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