Difference between revisions of "Details of 2021 Reference Genome Annotation Update R64.3"
| Line 22: | Line 22: | ||
|II | |II | ||
|[https://www.yeastgenome.org/locus/S000303802 YNCB0008W] aka GAL10-ncRNA | |[https://www.yeastgenome.org/locus/S000303802 YNCB0008W] aka GAL10-ncRNA | ||
| − | |New ncRNA antisense to GAL10 | + | |New ncRNA antisense to GAL10 |
| + | coordinates 276805..280645 | ||
|[https://www.yeastgenome.org/reference/S000128634 Houseley et al 2008] PMID:19061643, | |[https://www.yeastgenome.org/reference/S000128634 Houseley et al 2008] PMID:19061643, | ||
[https://www.yeastgenome.org/reference/S000131425 Pinskaya et al 2009] PMID:19407817, | [https://www.yeastgenome.org/reference/S000131425 Pinskaya et al 2009] PMID:19407817, | ||
| Line 29: | Line 30: | ||
|II | |II | ||
|YNCB0014W aka TBRT/XUT_2F-154 | |YNCB0014W aka TBRT/XUT_2F-154 | ||
| − | |New ncRNA antisense to TAT1 | + | |New ncRNA antisense to TAT1 |
| + | coordinates 376610..378633 | ||
|[https://www.yeastgenome.org/reference/S000250512 Awasthi et al 2020] PMID:32081726 | |[https://www.yeastgenome.org/reference/S000250512 Awasthi et al 2020] PMID:32081726 | ||
|- | |- | ||
|III | |III | ||
|RE/RE301 | |RE/RE301 | ||
| − | |New recombination enhancer | + | |New recombination enhancer |
| + | coordinates 29108..29809 | ||
|[https://www.yeastgenome.org/reference/S000045456 Wu and Haber 1996] PMID:8861911 | |[https://www.yeastgenome.org/reference/S000045456 Wu and Haber 1996] PMID:8861911 | ||
|- | |- | ||
Revision as of 16:06, 22 April 2021
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 | PMID:29320491 |
| V | HPA3/YEL066W | Moved translation start to Met19
old coordinates: 26667..27206 new coordinates: 26721..27206 |
PMID: 23775086 |
| VII | OTO1/YGR227C-A | New ORF | PMID: 25781884 |
| VII | ROK1/YGL171W | Added two new uORFs
uORF1: 182286..182407 uORF2: 182291..182329 |
PMID:20969870 |
| VIII | YHR052C-B | New ORF | PMID:29897761 |
| VIII | YHR054C-B | New ORF | PMID:29897761 |
| VIII | SUT169/YNCH0011W | New ncRNA | PMID:19169243, PMID:22226051, PMID:27292640, PMID:28977638 |
| X | YJR107C-A | New ORF | 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 | PMID:29897761 |
| XII | YLR379W-A | ||
| 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 | ||
| XIII | YNCM0001W aka PHO84 lncRNA | New ncRNA | PMID:18022365 |
| XIV | LTO1/YNL260C | Move start to Met37
old coords: 156859..157455 Crick new coords: 156859..157347 Crick |
PMID: 26182403 |
| XVI | YNCP0002W aka GAL4 lncRNA | New ncRNA | PMID: 22226051 |
