Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii

Brachat, Sophie; Dietrich, Fred S; Voegeli, Sylvia; Zhang, Zhihong; Stuart, Larissa; Lerch, Anita; Gates, Krista; Gaffney, Tom; Philippsen, Peter

doi:10.1186/gb-2003-4-7-r45

Table 2 Summary of different types of ORF extensions proposed for annotated S. cerevisiae ORFs

From: Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii

S. cerevisiae	Type*	Proposed reason^†	Extension size (codons)	Supporting evidence^‡
				Hemiascomycetes	C. albicans	S. pombe	N. crassa	S. cerevisiae ^§
YAL013W	3' extension	FS	57	++	++		++	Resequenced
YAR044W/YAR042W	Fusion	FS		++	++	++	++	Resequenced; duplication
YBL066C	3' intron	Intron + FS	3	+	+
YBL091C-A	5' intron	Intron	76	++	++	++
YBL104C	5' and 3' extensions	FS	128	++	++	++		Resequenced
YBR041W	3' extension	FS	46	++	++		++	Resequenced
YBR074W/YBR075W	Fusion	2FS		+	+	+	+	Resequenced
YBR098W/YBR100W	Fusion	FS		++	++		+
YBR157C	3' extension	1FS	149	++				Resequenced
YCL001W-A/YCL001W-B	Fusion	2FS						Duplication
YCL008C	3' extension	1FS	89					Resequenced [45]
YCL025C	3' extension	FS	38	++	++	+	++	gb: P25376; duplication
YCL069W	5' extension	PS	124	++	++	++	++
YDL115C	5' intron	Intron	113	++	++
YDR179W-A	5' extension	FS	138	++	++			gb: CAA86685
YDR474C/YDR475C	Fusion	2FS		++	++			Duplication
YDR494W	3' extension	FS	78	++	++
YER039C/YER039C-A	Fusion	PS	++	++	++	++		Duplication
YER066W	5' extension	PS	201	++	++	++	++
YFL007W/YFL006W	Fusion	FS	++	++		++		[46]
YFR038W	3' extension	FS	75	++	++	++
YFR040W	5' extension	FS	97	++				Duplication
YFR045W	5' extension	FS + PS	106	++	++	++	++	[47]
YGL046W/YGL045W	Fusion	3FS		++	++		+
YGL059W	3' extension	FS	46	++	++		++
YGL183C	5' intron	Intron	45	++	++
YGL211W	3' extension	3FS	164	++	++	++	++
YGR006W	3' extension	FS	32	++	++	++		[48]
YGR225W	3' extension	FS	31	++	++	++	++	[49]
YGR272C/YGR271C-A	Fusion	FS		++	++
YHR056C	5' extension	FS	51					gb: P38781; duplication
YHR079C-A	3' intron	Intron	45	++	++	++	++
YHR176W	3' extension	FS	67	++	++		++
YJL012C/YJL012C-A	Fusion	FS		++	++	++		Resequenced
YJL017W/YJL016W	Fusion	FS			++			Resequenced
YJL019W/YJL018W	Fusion	FS						Resequenced
YJL020C/YJL021C	Fusion	FS						Resequenced
YJL031C	5' intron	Intron	37	++	++	++	++
YJL108C/YJL107C	Fusion	FS		++	++	++	++	Resequenced
YJL159W	3' extension	FS	4	++	++			Resequenced; duplication
YJL160C	3' extension	FS	107	++	++			Resequenced; duplication
YJL178C	5' extension	FS	75	++	++			Resequenced
YJR013W	5' extension	FS	98	++	++	++	++	Resequenced
YKL033W-A	3' extension	FS	176	++		++	++	Resequenced
YKL199C/YKL198C	Fusion	FS		++	++	++	++	Resequenced; duplication
YKL207W	5' extension	FS	22	++	++	++		Resequenced
YKR004C	5' intron	Intron	85					5' RACE verified
YKR056W	5' extension	FS	21	++	++	++	++	Resequenced
YKR058W	5' extension	2FS	138	++	++			Resequenced [50]; duplication
YKR100C	3' extension	FS	114	++				Duplication
YKR103W/YKR104W	Fusion	PS		++	++	++	++
YLL017W/YLL016W	Fusion	FS			+			Duplication
YLL052C/YLL053C	Fusion	FS		++	++	++
YLR054C	5' intron	Intron	212	++	++
YLR205C	5' extension	2FS	44	++	++			Resequenced
YLR389C	3' extension	FS	40	++		++		Resequenced
YLR401C	3' extension	FS	59	++	++	++	++
YLR445W	3' intron	Intron	54
YML002W/YML003W	Fusion	FS		++	++		++
YML017W	5' intron	Intron	15					5' RACE verified
YMR084W/YMR085W	Fusion	FS		++	++	++	++	Duplication
YMR207C	5' extension	FS	59		++	++		Duplication
YMR269W	5' extension	FS	69	++	++			Resequenced
YNL083W	3' extension	FS	51	++	++	++	++	[47]
YNL130C	Other intron	Intron	21	++	++		++	[21]; duplication
YOL048C	5' intron	Intron	236	++	++			5' RACE verified; duplication
YOL163W/YOL162W	Fusion	PS+FS		++	++	++	++
YOR069W	5' extension	Annotation	364	++	++	++		gb: Q92331; duplication
YOR298C-A	5' extension	FS	92	++	++	++	++	Resequenced; gb: BAA33217
YPL109C	3' intron	Intron	47	++	++	++	++
YPR090W/YPR089W	Fusion	FS		++	++	++		Resequenced
YPR098C	5' intron	Intron	53	++	++

*Extension, ORF extension. ^†FS, frameshift; PS, premature STOP. ^‡Supporting evidence from other fungal sequences: ++ indicates that homology supports the corrected S. cerevisiae ORF; + indicates that weak homology supports the corrected S. cerevisiae ORF. ^§Supporting evidence from other S. cerevisiae sequences: from published work (reference given); from sequence databases (GenBank accession number); from this study (resequenced or 5'RACE); from duplicated S. cerevisiae sequences matching the proposed sequence (duplication).

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