S288C Sequence Changes

Updating the reference sequence is an on going project at SGD. All sequence updates are based on the re-sequencing of portions of the S288C strain background, and many also result in annotation changes, such as altering the start or stop codons.

Between May 1, 2004 and November 1, 2004, the sequence of 16 ORFs has been updated, 3 new ORFs have been added, and one ORF has been "merged" with a neighboring gene. These changes affect ORFs on the chromosomes listed below. For details on recent changes, scroll down, or click on the chromosome number.

I | II | III | IV | V | VII | VIII | XI | XVI
See the Table of Updates to the Systematic Sequence for comprehensive of all changes in the systematic sequence.

Chromosome I

OAF1/YAL051W
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted 2 deletions in YAL051W and this sequence error was confirmed in S288C by SGD. As a consequence of these changes, YAL051W was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 1062 to 1047 amino acids. (July 20, 2004) 

New:       TTTATTTGATTATGACTTTTTG-TTTGG-CAATGACTTTGCTTAAAAATTTTCTTTCCAA
           |||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||
OLD: 51666 TTTATTTGATTATGACTTTTTGGTTTGGGCAATGACTTTGCTTAAAAATTTTCTTTCCAA 51725

Chromosome II

SEF1/YBL066C
SGD re-sequenced this region in S288C and found that 37 nucleotide insertions and 4 nucleotide changes were necessary to correct the reference sequence. As a consequence of these changes, SEF1/YBL066C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 1,057 to 1,148 amino acids. (July 16, 2004) 
 
New:         1 TGTTTCCAGGAGTCTTCACGTTGTTTTCATTATCGATGGTTTGGAAGTTAGAAGAAGTTA 60  
               ||||||||||||||||||||||||||||||||||| ||||| |||   ||| ||||  
Current: 96777 TGTTTCCAGGAGTCTTCACGTTGTTTTCATTATCG-TGGTT-GGA---TAG-AGAA---- 96826 
 
New:        61 CAGTGTTAGTGCCCGTAGAAAATCGTTGGTTCGTTTTGTTGCTATTGATATCATTACTTT 120 
               |||||||||| |||||||||  |||| || |||||  ||| ||| ||||||||  |||||  
Current: 96827 CAGTGTTAGT-CCCGTAGAA--TCGT-GG-TCGTT--GTT-CTA-TGATATCA--ACTTT 96875 
 
New:       121 TGGAAAACAAGCTCAGAGGTGGATATGCCGTGCTTTTAGAGGAGCCGGGGTCGGAAACGA 180 
                ||||  ||| ||||||||||||||| |||| ||||||||||| |||||||||||  || 
Current: 96876 -GGAA--CAA-CTCAGAGGTGGATATCCCGT-CTTTTAGAGGA-CCGGGGTCGGA--CG- 96926 
 
New:       181 CGGAATGCAAATCTGTCATATTATTTGACTTCGAAGCAATCGGTGTACGTGAATGGGACA 240  
               |||||| |||  ||||||||| | |||||  |||| |||  |||||||||||||||||||  
Current: 96927 CGGAATCCAA--CTGTCATAT-A-TTGAC--CGAAACAAA-GGTGTACGTGAATGGGACA 96979

UBP13/YBL067C
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted the insertion of a single nucleotide; this sequence error was confirmed in S288C by SGD. As a consequence of this sequence change, UBP13/YBL067C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 688 to 747 amino acids. (July 13, 2004) 

 
New: TCGCTTTATAAAACAAAACATATGCTGTTGCCATATTTGGAGATTCACCTGTGAATTCTA 
     ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| 
Old: TCGCTTTATAAAACAAA-CATATGCTGTTGCCATATTTGGAGATTCACCTGTGAATTCTA

YBR062C
The work of Cliften et al. (Science (2003) 301(5629):71-6) predicted that there is a sequencing error in YBR062C: an single nucleotide should be deleted 100 nt upstream of the currently annotated start site. Assuming this sequence change, Cliften et al. further propose a new intron and 5' exon, and a framechange for this ORF. When spliced, this ORF would now encode a predicted protein of 180 amino acids. This sequence error was confirmed in S288C by SGD and the coordinates have been changed accordingly. (July 12, 2004) 

     New: AAAGTTTTGAAATAGACCTTGCAGTTGGGATCT-GACCTGTCTTCTCTGCTCCTCCTGTG 
          ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| 
     Old: AAAGTTTTGAAATAGACCTTGCAGTTGGGATCTTGACCTGTCTTCTCTGCTCCTCCTGTG

YBR108W
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted the insertion of a single G nt; this sequence error was confirmed in S288C by SGD. As a consequence of this sequence change, YBR108W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 848 to 947 amino acids. (July 09, 2004) 

 
New: CGGTTCGAAAAAAGTGAAGGACTCTAGCCCTGTTCCCTCAGATCTAGATGAAAAATATGT 
     ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| 
Old: CGGTTCGAAAAAAGTGAAG-ACTCTAGCCCTGTTCCCTCAGATCTAGATGAAAAATATGT

Chromosome III

YCR095W-A
The ORF YCR095W-A was added based on the work of Oshiro et al.(Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res (2002) 12(8):1210-20). (August 27, 2004)

Chromosome IV

YDR031W
The work of Kellis et al. (Nature. 2003 May 15;423(6937):241-54.) predicted insertion of a single nucleotide within the coding region of YDR031W; SGD resequenced this region and found that a single G nucleotide was necessary to correct the reference sequence. As a consequence of this schange, YDR031W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 117 - 121 amino acids. (July 22, 2004) 

 
New:    301 TAAAAATATTAAGCCTTCAATTAATGGAGTAAACTTGGAATTAATCAAGGACTGA 355 
            ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| 
Old: 503805 TAAAAATATTAAGCCTTCAATTAATGGAGTAAACTTG-AATTAATCAAGGACTGA 50385

YDR179W-A
The work of Brachat et al. (Genome Biol (2003) 4(7):R45) predicted insertion of a single nucleotide upstream of YDR179W-A; SGD resequenced this region and found that a single G nucleotide was necessary to correct the reference sequence. As a consequence of this schange, YDR179W-A was extended at the 5' end, altering the N-terminus (without changing the translation frame) and increasing the size of the predicted protein from 268 to 463 amino acids. (July 21, 2004) 

 
New:      1 TTTTATACAACACCAATTCCAGTTTAATTACCAAGTACCGAAGGCCAAATGCCTCAAATC 60 
            ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| 
Old: 819437 TTTTATACAACACCAATTCCAGTTTAATTACCAAGTACCGAAG-CCAAATGCCTCAAATC 819495

Chromosome V

YER090C-A
The ORF YER090C-A was added based on the work of Oshiro et al.(Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res (2002) 12(8):1210-20). (August 27, 2004)

Chromosome VII

YGL196W
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted insertion of a single nucleotide downstream of YGL196W; SGD resequenced this region, as well as the region upstream of YGL196W, and confirmed 5 separate sequence errors in the regions flanking YGL196W. SGD has corrected the reference sequence. As a consequence of these sequence changes, YGL196W was extended at both the 5' and the 3' ends, altering both the N-terminus and C-terminus (without changing the translation frame) and increasing the size of the predicted protein from 165 to 428 amino acids. (July 19, 2004) 

 
New:      1 GCAAAGGGAACTTTGAAACAATTGGGCCACGGACTTCCATTGGCTAAACGCACTACAAGA 60 
            ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||  
Old: 130070 GCAAAGGGAACTTTGAAACAATTGGGCCACGGACTTC-ATTGGCTAAACGCACTACAAGA 130128

AND 
 
New:    181 CCTCTTTTGAGCAATTTGTCAAGAAGGGTGAATAATTTTCAGGTTTTTG-TTGATAACAT 239 
            ||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||| 
Old: 130249 CCTCTTTTGAGAAATTTGTCAAGAAGGGTGAATAATTTTCAGGTTTTTGCTTGATAACAT 130308

AND 
 
New:    300 TTTTATCAAGGTTGATATGGGGACTAAGAGGGCAGGTCTTGCTTTCG-ACTCTCCAGAA 357 
            ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| 
Old: 130369 TTTTATCAAGGTTGATATGGGGACTAAGAGGGCAGGTCTTGCTTTCGGACTCTCCAGAA 130427

 
New:      1 ACGAAACTACTCCATTAAAATTAGGCAGCAAAATTGCCGTCCTTCCTCAA 50 
            ||||||||||||||||||| |||||||||||||||||||||||||||||| 
Old: 131029 ACGAAACTACTCCATTAAA-TTAGGCAGCAAAATTGCCGTCCTTCCTCAA 131077

YGL210W-A
The work of Brachat et al. (Genome Biol (2003) 4(7):R45) suggested potential sequence errors in and downstream of NCS6/YGL211W. SGD re-sequenced this region in S288C and found that two C nucleotide insertions and one nucleotide deletion were necessary to correct the reference sequence. As a consequence of these changes (1) NCS6/YGL211W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 193 to 359 amino acids and (2) YGL210W-A was merged into YGL211W. (July 20, 2004) 

 New:    1 CGTGGTGCTGCAAAGCTGGGCATATCTCACGTTGTCACCGGCCACAATGCAGACGATATG 60 
           ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| 
Old: 93023 CGTGGTGCTGCAAAG-TGGGCATATCTCACGTTGTCACCGGCCACAATGCAGACGATATG 93081

AND 
 
New:   181 TACCAAAAGGAAATTGTCCTGTATGCGCACTACATGAAGCTGGATTATTTTTCCACTGAG 240 
           ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| 
Old: 93202 TACCAAAAGGAAATTGTCCTGTATGCGCACTACATGAAGCTGGATTATTTTTC-ACTGAG 93260

AND 
 
New:   361 GCTAAAAAATCTAACGCTGGAAAGAGAGTCGTCAAATTTGTTGA-CGGCAATAGATGCGC 419 
           |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| 
Old: 93381 GCTAAAAAATCTAACGCTGGAAAGAGAGTCGTCAAATTTGTTGAACGGCAATAGATGCGC 93440

NCS6/YGL211W
The work of Brachat et al. (Genome Biol (2003) 4(7):R45) suggested potential sequence errors in and downstream of NCS6/YGL211W. SGD re-sequenced this region in S288C and found that two C nucleotide insertions and one nucleotide deletion were necessary to correct the reference sequence. As a consequence of these changes (1) NCS6/YGL211W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 193 to 359 amino acids and (2) YGL210W-A was merged into YGL211W. (July 20, 2004) 

 
New:      1 CGTGGTGCTGCAAAGCTGGGCATATCTCACGTTGTCACCGGCCACAATGCAGACGATATG 60 
           ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| 
Old: 93023 CGTGGTGCTGCAAAG-TGGGCATATCTCACGTTGTCACCGGCCACAATGCAGACGATATG 93081

AND 
 
New:   181 TACCAAAAGGAAATTGTCCTGTATGCGCACTACATGAAGCTGGATTATTTTTCCACTGAG 240 
           ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| 
Old: 93202 TACCAAAAGGAAATTGTCCTGTATGCGCACTACATGAAGCTGGATTATTTTTC-ACTGAG 93260

AND 
 
New:   361 GCTAAAAAATCTAACGCTGGAAAGAGAGTCGTCAAATTTGTTGA-CGGCAATAGATGCGC 419 
           |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| 
Old: 93381 GCTAAAAAATCTAACGCTGGAAAGAGAGTCGTCAAATTTGTTGAACGGCAATAGATGCGC 93440

MTO1/YGL236C
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted insertion of a single nucleotide; this sequence error was confirmed in S288C by SGD. As a consequence of this sequence change, MTO1/YGL236C was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 679 to 669 amino acids. (July 15, 2004) 

 
New: ATATTTACATGACTGGTTGGCTTGGCTTCCGTGCCACACGGTAGAGTTCAAATAGGGCTG 
     ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| 
Old: ATATTTACATGACTGGTTGGCTTGGCTTC-GTGCCACACGGTAGAGTTCAAATAGGGCTG

YGR161W-C
The ORF YGR161W-C was added per Blandin et al. (Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett (2000) 487(1):31-6). Note that this ORF was originally published using the systematic name "YGR161W-A;" however, the systematic name "YGR161W-A" had already been used to refer to a TyA Gag protein downstream of the new ORF predicted by Blandin et al. (August 27, 2004)

PHB2/YGR231C
The work of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) predicted insertion of a single nucleotide; this sequence error was confirmed in S288C by SGD. As a consequence of this sequence change, PHB2/YGR231C was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 315 to 310 amino acids. (July 15, 2004) 

 
New: TAAAGATAATATCTAGCCTTCGCTATTTATTTG-CCCCTTCCATCGATTCTTGCATCCAC 
     ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| 
Old: TAAAGATAATATCTAGCCTTCGCTATTTATTTGACCCCTTCCATCGATTCTTGCATCCAC

Chromosome VIII

YHR131C
The work of Kellis et al. (Nature. 2003 May 15;423(6937):241-54.) proposed an indel that would extend the YHR131C reading frame and the sequence error was confirmed in S288C by SGD. As a consequence of this change, YHR131C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 840 to 850 amino acids. In addition, YHR131W-A was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 115 to 81 amino acids. (July 26, 2004) 

New:        TAATTTGCCCTCTATTGGCAGAGCCATCCTTAACAAACGAACAACTTGTATGCACGATGT
            |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Old: 367868 TAATTTGCCCTCTATTGGCAGAGC-ATCCTTAACAAACGAACAACTTGTATGCACGATGT 367926

YHR131W-A
The work of Kellis et al. (Nature. 2003 May 15;423(6937):241-54.) proposed an indel that would extend the YHR131C reading frame and the sequence error was confirmed in S288C by SGD. As a consequence of this change, YHR131C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 840 to 850 amino acids. In addition, YHR131W-A was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 115 to 81 amino acids. (July 26, 2004) 

New:        TAATTTGCCCTCTATTGGCAGAGCCATCCTTAACAAACGAACAACTTGTATGCACGATGT
            |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Old: 367868 TAATTTGCCCTCTATTGGCAGAGC-ATCCTTAACAAACGAACAACTTGTATGCACGATGT 367926

Chromosome XI

OMA1/YKR087C
The work of Kellis et al. (Nature. 2003 May 15;423(6937):241-54.) predicted a single nucleotide insertion upstream of OMA1/YKR087C. SGD resequenced this region and found that a single T nucleotide was necessary to correct the reference sequence. As a consequence of this change, OMA1/YKR087C was extended at the 5' end, altering the N-terminus (without changing the translation frame for most of the protein) and increasing the size of the predicted protein from 314 to 345 amino acids. (July 23, 2004) 

New:      1 CCATTATTAAATCGACGATATGAAGGACCATTGTCATAGCGGTAACATCGCGTTAACTGA 60 
            |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| 
Old: 603735 CCATTATTAAATCGACGATATGAAGGACCATTGTCATAGCGG-AACATCGCGTTAACTGA 603793

SRL3/YKR091W
The works of Kellis et al. (Nature. 2003 May 15;423(6937):241-54.) and Cliften et al. (Science (2003) 301(5629):71-6) predicted a single nucleotide insertion upstream of SRL3/YKR091W. SGD resequenced this region and found that a single G nucleotide was necessary to correct the reference sequence. As a consequence of this change, SRL3/YKR091W was extended at the 5' end, altering the N-terminus (without changing the translation frame) and increasing the size of the predicted protein from 152 to 246 amino acids. (July 23, 2004) 

New:     1 GATACTGAATCTAACAGCCTTCTGGCGACGCCGGCAAGGAAATATTTCAAAACTTCAATA 60 
            |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| 
Old: 611256 GATACTGAATCTAACAGCCTTCTG-CGACGCCGGCAAGGAAATATTTCAAAACTTCAATA 611314

Chromosome XVI

YPL109C
The works of Kellis et al (Nature. 2003 May 15;423(6937):241-54.) and Cliften et al (Science 2003 Jul 4;301(5629):71-6.) predicted multiple insertions and deletions in YPL109C, and the sequence errors were confirmed in S288C by SGD. As a consequence of these changes, YPL109C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 590 to 657 amino acids. (July 21, 2004) 

New:        TGTTTTGGAAACGAATTTT-GTGTCAAATAAAAAGCAATTGACGTAGGTATTATGAACTG
            ||||||||||||||||||| |||||||| |||||||||||| ||||||||||||||||||
Old: 347246 TGTTTTGGAAACGAATTTTTGTGTCAAA-AAAAAGCAATTG-CGTAGGTATTATGAACTG 347303
Return to SGD
Send a Message to the SGD Curators