Table 2

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

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).

Brachat et al. Genome Biology 2003 4:R45   doi:10.1186/gb-2003-4-7-r45

Open Data