Difference between revisions of "Details of 2024 Reference Genome Annotation Update R64.5"

From SGD-Wiki
Jump to: navigation, search
(Created page with "The ''S. cerevisiae'' strain S288C reference genome annotation was updated. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome se...")
 
(→‎R64.5 Annotation update summary)
 
(4 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
==R64.5 Annotation update summary==
 
==R64.5 Annotation update summary==
 
This annotation update included (details in table below):
 
This annotation update included (details in table below):
−
*new ORFs:
+
*new ORFs: [https://www.yeastgenome.org/locus/YDL204W-A YDL204W-A], [https://www.yeastgenome.org/locus/YFR035W-A YFR035W-A], [https://www.yeastgenome.org/locus/YGR016C-A YGR016C-A], [https://www.yeastgenome.org/locus/YMR106W-A YMR106W-A], [https://www.yeastgenome.org/locus/YNL040C-A YNL040C-A], [https://www.yeastgenome.org/locus/YNL155C-A YNL155C-A]
−
*new uORFs for 3 ORFs:  
+
*new uORFs for existing ORFs: [https://www.yeastgenome.org/locus/ATG12 ATG12/YBR217W], [https://www.yeastgenome.org/locus/ATG19 ATG19/YOL082W], [https://www.yeastgenome.org/locus/ATG5 ATG5/YPL149W], [https://www.yeastgenome.org/locus/ATG13 ATG13/YPR185W]
−
*1 ORF upgraded from Dubious to Verified:
+
*move start downstream: [https://www.yeastgenome.org/locus/EFM4 EFM4/YIL064W]
 +
*ORF upgraded from Dubious to Verified: [https://www.yeastgenome.org/locus/YIL059C YIL059C]
 +
 
 +
==R64.5 Annotation update details==
 +
{| border="1" style="border-collapse:collapse; width:90%" cellpadding="3"
 +
|-
 +
! style="background: #D8D8D8" | Chr
 +
! style="background: #D8D8D8" | Feature
 +
! style="background: #D8D8D8" | Description of change
 +
! style="background: #D8D8D8" | Reference
 +
|-
 +
|II
 +
|[https://www.yeastgenome.org/locus/ATG12 ATG12/YBR217W]
 +
|New uORF chrII:657824..657835, partially overlaps CDS
 +
|[https://www.yeastgenome.org/reference/S000314966 Yang Y, et al. (2023)] PMID:35363116
 +
|-
 +
|IV
 +
|[https://www.yeastgenome.org/locus/YDL204W-A YDL204W-A]
 +
|New ORF chrIV:94133..94285
 +
|[https://www.yeastgenome.org/reference/S000343589 Wacholder A, et al. (2023)] PMID:37164009
 +
|-
 +
|VI
 +
|[https://www.yeastgenome.org/locus/YFR035W-A YFR035W-A]
 +
|New ORF chrVI:226260..226550
 +
|[https://www.yeastgenome.org/reference/S000346762 Wacholder A and Carvunis AR (2023)] PMID:38048358
 +
|-
 +
|VII
 +
|[https://www.yeastgenome.org/locus/YGR016C-A YGR016C-A]
 +
|New ORF chrVII:523353..523246
 +
|[https://www.yeastgenome.org/reference/S000343589 Wacholder A, et al. (2023)] PMID:37164009, 
 +
[https://www.yeastgenome.org/reference/S000346184 Chang S, et al. (2023)] PMID:37927910
 +
|-
 +
|IX
 +
|[https://www.yeastgenome.org/locus/EFM4 EFM4/YIL064W]
 +
|Move start 84 nucleotides downstream, new coordinates chrIX:242027..242716
 +
|[https://www.yeastgenome.org/reference/S000347127 Hamey JJ, et al. (2024)] PMID:38199565
 +
|-
 +
|IX
 +
|[https://www.yeastgenome.org/locus/YIL059C YIL059C]
 +
|Change ORF qualifier from Dubious to Verified because stable translation product detected
 +
|[https://www.yeastgenome.org/reference/S000346762 Wacholder A and Carvunis AR (2023)] PMID:38048358
 +
|-
 +
|XIII
 +
|[https://www.yeastgenome.org/locus/YMR106W-A YMR106W-A]
 +
|New ORF chrXIII:480924..481187
 +
|[https://www.yeastgenome.org/reference/S000346762 Wacholder A and Carvunis AR (2023)] PMID:38048358
 +
|-
 +
|XIV
 +
|[https://www.yeastgenome.org/locus/YNL040C-A YNL040C-A]
 +
|New ORF chrXIV:552558..552478
 +
|[https://www.yeastgenome.org/reference/S000343589 Wacholder A, et al. (2023)] PMID:37164009
 +
|-
 +
|XIV
 +
|[https://www.yeastgenome.org/locus/YNL155C-A YNL155C-A]
 +
|New ORF chrXIV:342135..341911
 +
|[https://www.yeastgenome.org/reference/S000346762 Wacholder A and Carvunis AR (2023)] PMID:38048358
 +
|-
 +
|XV
 +
|[https://www.yeastgenome.org/locus/ATG19 ATG19/YOL082W]
 +
|New uORF chrXV:168632..168679
 +
|[https://www.yeastgenome.org/reference/S000314966 Yang Y, et al. (2023)] PMID:35363116
 +
|-
 +
|XVI
 +
|[https://www.yeastgenome.org/locus/ATG5 ATG5/YPL149W]
 +
|4 new uORFs: chrXVI:271236..271277, chrXVI:271252..271302, chrXVI:271299..271307, chrXVI:271302..271307
 +
|[https://www.yeastgenome.org/reference/S000314966 Yang Y, et al. (2023)] PMID:35363116
 +
|-
 +
|XVI
 +
|[https://www.yeastgenome.org/locus/ATG13 ATG13/YPR185W]
 +
|New uORF chrXVI:907211..907351, partially overlaps CDS
 +
|[https://www.yeastgenome.org/reference/S000314966 Yang Y, et al. (2023)] PMID:35363116
 +
|-
 +
|}

Latest revision as of 11:33, 18 June 2024

The S. cerevisiae strain S288C reference genome annotation was updated. The new genome annotation is release R64.5.1, dated 2024-05-29. Note that the underlying genome sequence itself was not altered. The chromosome sequences remain stable.

R64.5 Annotation update summary

This annotation update included (details in table below):

R64.5 Annotation update details

Chr Feature Description of change Reference
II ATG12/YBR217W New uORF chrII:657824..657835, partially overlaps CDS Yang Y, et al. (2023) PMID:35363116
IV YDL204W-A New ORF chrIV:94133..94285 Wacholder A, et al. (2023) PMID:37164009
VI YFR035W-A New ORF chrVI:226260..226550 Wacholder A and Carvunis AR (2023) PMID:38048358
VII YGR016C-A New ORF chrVII:523353..523246 Wacholder A, et al. (2023) PMID:37164009,

Chang S, et al. (2023) PMID:37927910

IX EFM4/YIL064W Move start 84 nucleotides downstream, new coordinates chrIX:242027..242716 Hamey JJ, et al. (2024) PMID:38199565
IX YIL059C Change ORF qualifier from Dubious to Verified because stable translation product detected Wacholder A and Carvunis AR (2023) PMID:38048358
XIII YMR106W-A New ORF chrXIII:480924..481187 Wacholder A and Carvunis AR (2023) PMID:38048358
XIV YNL040C-A New ORF chrXIV:552558..552478 Wacholder A, et al. (2023) PMID:37164009
XIV YNL155C-A New ORF chrXIV:342135..341911 Wacholder A and Carvunis AR (2023) PMID:38048358
XV ATG19/YOL082W New uORF chrXV:168632..168679 Yang Y, et al. (2023) PMID:35363116
XVI ATG5/YPL149W 4 new uORFs: chrXVI:271236..271277, chrXVI:271252..271302, chrXVI:271299..271307, chrXVI:271302..271307 Yang Y, et al. (2023) PMID:35363116
XVI ATG13/YPR185W New uORF chrXVI:907211..907351, partially overlaps CDS Yang Y, et al. (2023) PMID:35363116
Retrieved from "https://wiki.yeastgenome.org/index.php?title=Details_of_2024_Reference_Genome_Annotation_Update_R64.5&oldid=406888"