Chromosome XII History |
| SEQUENCE CHANGES, including any resulting annotation changes | Jump to: Annotation changes |
Date  | Affected Features | Start Coordinate of Change | End Coordinate of Change | Type of Change | Old Sequence | New Sequence |
|---|---|---|---|---|---|---|
| 2011-02-03 | YLL054C | 32902 | 32902 | Insertion | A | |
A single nucleotide was inserted very near the 3' end of ORF YLL054C, altering its coding sequence. The start and most of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 74 amino acids longer.
New 32881 AATTGTGGATTGTTTAATTTTGATGTGAACGAAAAGGACTTATCCCTTCCCATACCCCAT 32940
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Old 32881 AATTGTGGATTGTTTAATTTTG-TGTGAACGAAAAGGACTTATCCCTTCCCATACCCCAT 32939Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology.  | ||||||
| 2011-02-03 | YLR407W | 933639 | 933639 | Insertion | G | |
A single G nucleotide was inserted within the ORF YLR407W near its 3' end, altering its coding sequence. The start and vast majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now one amino acid shorter.
New 933597 AATGCAGGCTGGACGGAAACGAGAAAGTGGGCTAATGCTGCCAAGGGCATGCCATGACTG 933656
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Old 933596 AATGCAGGCTGGACGGAAACGAGAAAGTGGGCTAATGCTGCCAA-GGCATGCCATGACTG 933654Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR402W | 924691 | 924691 | Insertion | G | |
A single G nucleotide was inserted within the ORF YLR402W near its 5' end, necessitating a change in annotation to a downstream start codon. The sequence change makes the longer version of the protein no longer possible in the reference sequence. The stop and reading frame remain the same, but the annotated protein is now 108 amino acids shorter, less than half its original size.
New: 924657 TTAAGTCTCTTCATCCCGTGTACTATTACCCGACAGGTTTCTGCGGCATGTTCTGTGGAA 924716
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Old: 924657 TTAAGTCTCTTCATCCCGTGTACTATTACCCGACA-GTTTCTGCGGCATGTTCTGTGGAA 924715Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR313C | 760764 | 760764 | Insertion | CC | |
A GG dinucleotide was inserted within the ORF SPH1/YLR313C near its 3' end, altering its coding sequence. The start and majority of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 131 amino acids shorter.
New 760738 CTTGAACATCATTCAAAATGCCCTGCCTGCCATAGGAAGAACAACCATTGATTTACTCTC 760797
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Old 760740 CTTGAACATCATTCAAAATGCCCTG--TGCCATAGGAAGAACAACCATTGATTTACTCTC 760797Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR318W | 767026 | 767027 | Substitution | TC | CT |
Nucleotide change(s) in the coding region of EST2/YLR318W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 162 is now Alanine rather than Valine.
New 766978 AAATCGTGGGTAACAGATGTAACGAACCTCATCTGCCGCCCAAATGGGCTCAACGATCATCCTCATCATC 767047
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Old 766978 AAATCGTGGGTAACAGATGTAACGAACCTCATCTGCCGCCCAAATGGGTCCAACGATCATCCTCATCATC 767047Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR314C | 762846 | 762846 | Substitution | A | T |
Nucleotide change(s) in the coding region of CDC3/YLR314C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 431 is now Glutamine rather than Leucine.
New 762828 TGTAAAGTTTTTTCTTCTTGTTGTTTAGATATTGGATCGAACTCTTTGAAAACTGAATTATCTTGCTTAA 762897
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Old 762828 TGTAAAGTTTTTTCTTCTAGTTGTTTAGATATTGGATCGAACTCTTTGAAAACTGAATTATCTTGCTTAA 762897Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR034C | 210771 | 210771 | Substitution | A | T |
A single nucleotide substitution was made within ORF SMF3/YLR034C. Note that the protein sequence was not changed.
New 210719 ATGAACAACCATCAACTTTCTATTTGCGGTAAAATAAATTAAAGGAGCGGATACGATTGGTAAAATTAAG 210788
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Old 210720 ATGAACAACCATCAACTTTCTATTTGCGGTAAAATAAATTAAAGGAGCGGAAACGATTGGTAAAATTAAG 210789Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR162W-A, YLR163C | 491154 | 491154 | Deletion | C | |
A single nucleotide deletion was made in the intergenic region between ORFs RRT15/YLR162W-A and MAS1/YLR163C.
New 491099 TGAAGAGGTAGGTACATATTCATTGGCAGATATTCTACAATGCAATTATTATGA-CCAATCACACAGTAT 491167
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Old 491100 TGAAGAGGTAGGTACATATTCATTGGCAGATATTCTACAATGCAATTATTATGACCCAATCACACAGTAT 491169Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR346C, YLR347C | 822958 | 822958 | Insertion | G | |
A single nucleotide insertion was made in the intergenic region between ORFs YLR346C and KAP95/YLR347C.
New 822948 TCAGCAGGTGCGGCTGTGCCTTTTCACTTTCAGCTAAGATGTTTGCAAGCAAGAATTAACAGATAAGCCG 823017
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Old 822948 TCAGCAGGTGC-GCTGTGCCTTTTCACTTTCAGCTAAGATGTTTGCAAGCAAGAATTAACAGATAAGCCG 823016Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR412C-A, YLR412W | 949230 | 949230 | Insertion | C | |
A single nucleotide insertion was made in the intergenic region bewteen ORFs BER1/YLR412W and YLR412C-A.
New 949197 TCATTCACTACATAGTACTTTATAACTAAACTGTAACCTTTCAGGGCATCGTAACCTGAC 949256
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Old 949195 TCATTCACTACATAGTACTTTATAACTAAACTGTAA-CTTTCAGGGCATCGTAACCTGAC 949253Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR277C, YLR278C | 699963 | 699963 | Substitution | G | A |
A single nucleotide substitution was made in the intergenic region between ORFs YSH1/YLR277C and YLR278C.
New 699948 AAAAAAAAAAAAAAGGAATGAGTTTGTACATACTATTATATTAATGTAGTATCACGTTAAAAAGCCGTAG 700017
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Old 699950 AAAAAAAAAAAAAGGGAATGAGTTTGTACATACTATTATATTAATGTAGTATCACGTTAAAAAGCCGTAG 700019Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR447C, YLR448W | 1028607 | 1028607 | Insertion | G | |
A single nucleotide insertion was made in the intergenic region between ORFs VMA6/YLR447C and RPL6B/YLR448W.
New 1028577 TAACCTGGACTTGCCGTGCTAAGTCGGCCTTCTAGGCTGCGCTTCCGTTCAGCATCGTTT 1028636
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Old 1028574 TAACCTGGACTTGCCGTGCTAAGTCGGCCTTCTA-GCTGCGCTTCCGTTCAGCATCGTTT 1028632Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR449W, YLR450W | 1032533 | 1032533 | Deletion | G | |
A single nucleotide deletion was made in the intergenic region between ORFs FPR4/YLR449W and HMG2/YLR450W.
New 1032527 GTTATAGTAA-GACACTTCAGTGAGAAATTAATCTGACTTACTTTTACTTAATTGTGTTCTTTCCAAATT 1032595
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Old 1032523 GTTATAGTAAGGACACTTCAGTGAGAAATTAATCTGACTTACTTTTACTTAATTGTGTTCTTTCCAAATT 1032592Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR024C, YLR025W | 193483 | 193483 | Substitution | A | C |
A single nucleotide substitution was made in the intergenic region between ORFs UBR2/YLR024C and SNF7/YLR025W.
New 193439 ATTGAAAGTATGAATGCGTTGATTATTGGGTTTCTCCCCACAGCTGTACATTGACGATGC 193498
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Old 193440 ATTGAAAGTATGAATGCGTTGATTATTGGGTTTCTCCCCACAGATGTACATTGACGATGC 193499Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR024C | 192416 | 192416 | Substitution | C | T |
A single nucleotide substitution was made within ORF UBR2/YLR024C. Note that the protein sequence was not changed.
New 192359 TCTTCTAAAGCCTTCGTTATTGAGATTGCATATTCAACCGGTGTATTCAAAATTCTTGTTATTGTAGATG 192428
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Old 192360 TCTTCTAAAGCCTTCGTTATTGAGATTGCATATTCAACCGGTGTATTCAAAATTCTCGTTATTGTAGATG 192429Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | ||||||
| YLR023C, YLR024C | ||||||
| 187423 | 187423 | Deletion | A | |||
| 187394 | 187394 | Deletion | A | |||
Two separate single nucleotide deletions were made in the intergenic region between ORFs IZH3/YLR023C and UBR2/YLR024C.
New 187381 ACCTTATCCATCAA-CACTTTCTCCATTTCCTGCAGGGTAAAA-AGAAAAGTGAAGTCAC 187438
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Old 187380 ACCTTATCCATCAAACACTTTCTCCATTTCCTGCAGGGTAAAAAAGAAAAGTGAAGTCAC 187439Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR022C, YLR023C | 185062 | 185062 | Substitution | G | A |
A single nucleotide substitutuion was made in the intergenic region between ORFs SDO1/YLR022C and IZH3/YLR023C.
New 185041 ATATATACAAGGCACTGAGCAGAACAATACACGCTAAGTTTTGTTCTTTCATGAGGTCAT 185100
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Old 185040 ATATATACAAGGCACTGAGCAGGACAATACACGCTAAGTTTTGTTCTTTCATGAGGTCAT 185099Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR378C, YLR380W | 878171 | 878171 | Deletion | G | |
A single nucleotide deletion was made in the intergenic region between ORFs SEC61/YLR378C and CSR1/YLR380W.
New 878158 AAATCTTGGCACTT-GTCACTTACGCTCCTTTAAACAAAATCAAACATACAAATATACGG 878216
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Old 878157 AAATCTTGGCACTTGGTCACTTACGCTCCTTTAAACAAAATCAAACATACAAATATACGG 878216Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR451W, YLR452C | 1038769 | 1038769 | Deletion | C | |
A single nucleotide deletion was made in the intergenic region between ORFs LEU3/YLR451W and SST2/YLR452C.
New 1038716 TTTTAATGAATGAATTTGCGTTCAATCCCAAGGTTTAAAGTCCTTTTCTTTTTTTG-CGTAATGTTTACT 1038784
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Old 1038713 TTTTAATGAATGAATTTGCGTTCAATCCCAAGGTTTAAAGTCCTTTTCTTTTTTTGCCGTAATGTTTACT 1038782Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2011-02-03 | YLR309C | 750224 | 750224 | Substitution | C | T |
A single nucleotide substitution was made within ORF IMH1/YLR309C. Note that the protein sequence was not changed.
New 750178 TCACTAAATTGTTTAACTTGTTCCTCCAAGTAACTCACAGTTTTTTCCTTTTGTTTATAA 750237
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Old 750180 TCACTAAATTGTTTAACTTGTTCCTCCAAGTAACTCACAGTTTTCTCCTTTTGTTTATAA 750239Dietrich F (2011) Personal Communication, An updated S. cerevisiae reference genome: Resequencing of S288C using NextGen sequencing technology. | ||||||
| 2006-01-09 | YLR401C | 922648 | 922648 | Insertion | G | |
Based on the automated comparison of related fungi, Kellis et al. and Brachat et al. suggest that the stop site for YLR401C be moved 176 nt downstream. SGD confirmed the insertion of a single G nt. and have updated the systematic sequence accordingly. As a consequence of this sequence change, DUS3/YLR401C was extended on the 3' end, altering the C-terminus and increasing the size of the predicted protein from 609 to 668 amino acids
New: 922634 ACAAATACCCATGGGGACATACCTATGAAAAA 922665
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Old: 922634 ACAAATACCCATGGG-ACATACCTATGAAAAA 922664
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54     Brachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 | ||||||
| 2004-02-05 | ||||||
| YLR205C | ||||||
| 553633 | 553633 | Insertion | C | |||
| 553548 | 553548 | Insertion | G | |||
Brachat et al. 2003 predicted and confirmed the insertion of two nucleotides in Chromosome XII - a G after the G at 553548, and a C after the C at 553633. As a consequence of these sequence changes, HMX1/YLR205C was extended at the 5' end, increasing the size of the protein from 273 amino acids to 317 amino acids. New: ACATAATAGTACGCCAGAATACCCTGTCTGTATATAAAGCCATGTCTCATGGCGATGGCCBrachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 | ||||||
| 2004-02-04 | YLR312C-B, YLR313C | 760763 | 760764 | Deletion | CC | |
| Roemer et al confirmed the deletion of two C nucleotides in SPH1/YLR313C in an S288C strain background. As a consequence of this sequence change, SPH1/YLR313C was extended at the 3' and merged with an adjacent ORF, YLR312C-B, that was in the same frame. This change increased the size of the Sph1p from 530 amino acids to 661 amino acids. Roemer et al also confirmed other laboratory strain backgrounds, such as W303-derived strains, do have the additional two nucleotides and encode the shorter protein.
New: CTTGAACAATTTTGATTTAGAGGCTTGAACATCATTCAAAATGCCCTG--TGCCATAGGARoemer T, et al. (1998) The Spa2-related protein, Sph1p, is important for polarized growth in yeast. J Cell Sci 111 ( Pt 4)():479-94 | ||||||
| 2004-02-04 | YLR389C | 899751 | 899751 | Insertion | T | |
Brachat et al. 2003 predicted and confirmed the insertion of a single T nucleotide in YLR389C. As a consequence of this sequence change, YLR389C was extended at the 3' end, increasing the size of the predicted protein from 988 amino acids to 1027 amino acids.Query: GCTCTTTGTTTTCCACTTGAGATTTCAAATGTAGAATCAACTTCGATGCGTTCTCGCTCABrachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 | ||||||
| 2001-06-12 | YLR312W-A | 759511 | 759511 | Insertion | C | |
Inserted one C nucleotide after the C at chromosomal coordinate 759511. This insertion is in the intron of YLR312W-A and therefore does not affect YLR312W-A translation.
Old: 759481 TGGAAAATAGCATGATGTTTATATCGCGTTC-TTGCGGAGACCCGTTACTGCTTTGAACT 759539
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New: 759481 TGGAAAATAGCATGATGTTTATATCGCGTTCCTTGCGGAGACCCGTTACTGCTTTGAACT 759540
Kitakawa M, et al. (1997) Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae. Eur J Biochem 245(2):449-56 | ||||||
| 1997-07-30 | YLR028C | 199680 | 199680 | Insertion | T | |
A single T nucleotide was inserted before the T at chromosomal coordinate 199680 within the ORF ADE16/YLR028C. At the same time this sequence change was made, the stop site for YLR028C was moved downstream 110 nucleotides.
New: 199649 CTTTACACCAGACTGCACAGCTCTATAAACGTTGTCTGGGAAGGGAAAGAACGCATCGGA 199708
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Old: 199649 CTTTACACCAGACTGCACAGCTCTATAAACGT-GTCTGGGAAGGGAAAGAACGCATCGGA 199707
Note that this ORF is on the Crick strand, which is complementary to the sequence shown above. | ||||||
| ANNOTATION CHANGES without sequence changes | Jump to: Sequence changes |
Date  | Affected Features |
|---|---|
| 1997-07-30 | YLR390W-A, YLR391W |
| YLR391W was an ORF that was named in the original sequence of Chromosome XII. Since it was completely contained in a larger ORF with a better codon bias, it was deleted from SGD and GenBank in favor of the larger ORF, YLR391W-A. | |
| 1999-07-17 | YLR362W |
| The start site of YLR362W was moved 63 nucleotides downstream. | |
| 1999-07-17 | YLR406C |
| The intron of YLR406C was moved 2 nucleotides downstream, changing the relative coordinates of the coding sequence from 1-55..405-691 to 1-57..407-691, and amino acid 19 from lysine to arginine. | |
| 2000-07-14 | YLR211C |
| The start site of YLR211C was moved 317 nucleotides upstream, and at the same time an intron was added at relative coordinates 19-77. The old chromosomal coordinates of the coding sequence were 564213-563791, and the new chromosomal coordinates of the coding sequence are now 564531-564514..564454-563792. | |
| 2000-07-14 | YLR093C |
| The start site of YLR093C was moved 147 nucleotides upstream, and at the same time an intron was added at relative coordinates 17-157. The chromosomal coordinates for the coding region have changed from 327268-326513 to 327416-327401..327259-326514. | |
| 2000-07-22 | YLR316C |
| The start site of YLR316C was moved 601 nucleotides upstream, and at the same time two separate introns were added at new relative coordinates 110-177 and 230-285. The chromosomal coordinates for the coding region have changed from 765755-765264 to 766357-766249..766180-766129..766072-765265. | |
| 2000-08-11 | YLR337C |
| Old name: YLR337W; new name: YLR337C; date: 2/10/2000; old coord: ChrXII; SGDID: Unknown; old change found in mips | |
| 2001-03-09 | snR79 |
| Changed from W -> C: old start coord: 348428; old stop coord: 348511 new start coord: 348511; new stop coord: 348428 (Eric Steinmetz, personal communication; Qu et al.)Qu LH, et al. (1999) Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol Cell Biol 19(2):1144-58 | |
| 2003-07-29 | YLL019W-A, YLL066W-A, YLL066W-B, YLL067W-A, YLR120W-A, YLR154W-A, YLR154W-E, YLR157W-D, YLR157W-E, YLR286W-A, YLR299C-A, YLR347W-A, YLR399W-A, YLR406C-A, YLR437C-A, YLR466C-A, YLR466C-B, YLR467C-A |
Thanks to Kumar et al. for providing the coordinates of the following Chromosome XII ORFs: YLL019W-A, YLL066W-A, YLL066W-B, YLL067W-A, YLR406C-A, YLR437C-A, YLR466C-A, YLR466C-B, YLR467C-A, YLR120W-A, YLR154W-A, YLR154W-E, YLR157W-D, YLR157W-E, YLR286W-A, YLR299C-A, YLR347W-A, and YLR399W-A.Kumar A, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63  | |
| 2003-07-29 | YLR154W-F, YLR163W-A, YLR361C-A, YLR364C-A |
| Thanks to
Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of the following Chromosome XII ORFs: YLR154W-F, YLR163W-A, YLR361C-A, and YLR364C-A.Basrai MA, et al. (1999) NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae. Mol Cell Biol 19(10):7041-9 Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51 Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20 | |
| 2003-07-29 | YLR264C-A |
| Thanks to MIPS for providing the coordinates of YLR264C-A. | |
| 2003-07-29 | YLR307C-A |
| Thanks to Brachat et al. for providing the coordinates of YLR307C-A.Brachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 | |
| 2003-07-29 | YLL006W-A, YLR154C-G, YLR154C-H, YLR154W-B, YLR156C-A, YLR157C-C, YLR159C-A, YLR162W-A, YLR222C-A, YLR285C-A, YLR312C-B, YLR342W-A, YLR412C-A |
| Thanks to Kessler et al. for providing the coordinates of the following Chromosome XII ORFs: YLR285C-A, YLR312C-B, YLR342W-A, YLR412C-A, YLL006W-A, YLR154C-G, YLR154C-H, YLR154W-B, YLR156C-A, YLR157C-C, YLR159C-A, YLR162W-A, and YLR222C-A.Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71 | |
| 2003-09-09 | TEL12L, TEL12L-TR1, TEL12L-TR2, TEL12L-TR3, TEL12L-XC, TEL12L-XR, TEL12L-YP1, TEL12L-YP2, TEL12R, TEL12R-TR1, TEL12R-TR2, TEL12R-XC, TEL12R-XR, TEL12R-YP1, TEL12R-YP2 |
| The chromosomal locations for TEL12R, TEL12R-TR1, TEL12R-TR2, TEL12R-XC, TEL12R-XR, TEL12R-YP1, TEL12R-YP2, TEL12L-YP2, TEL12L-TR2, TEL12L-XC, TEL12L-XR, TEL12L-YP1, TEL12L-TR3, TEL12L-TR1, and TEL12L were generously provided by Ed Louis and Dave Barton (University of Leicester, UK). | |
| 2003-09-22 | YLR435W |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for TSR2/YLR435W be moved 132 nt (44 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine; 3) Although S. paradoxus, S. mikatae, and S. bayanus have upstream ATGs, there are insertions and deletions which cause frame shifts in between the first and second ATGs; 4) Protein sequence comparison with the nr dataset show there are no sequence similarities between the first and second ATG. All hits occur after the 2nd ATG.Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2003-09-22 | YLR012C |
| The automated comparison of closely related Saccharomyces species suggests that the start site for YLR012C be moved 69 nt (23 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine; 3) The first ATG and the translation frame are not conserved in the related species.Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2003-09-22 | YLR027C |
| The automated comparison of closely related Saccharomyces species suggests that the start site for AAT2/YLR027C be moved 42 nt (14 codons) downstream. This suggestion was reviewed and accepted by SGD curators. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine; 3) The first ATG is not conserved in the related species; 4) Sequencing of the entire protein reported the following sequence in the amino terminus: SATLFNNIELL (Cronin VB, et al.).Cronin VB, et al. (1991) The amino acid sequence of the aspartate aminotransferase from baker's yeast (Saccharomyces cerevisiae). Biochem J 277 ( Pt 2)():335-40 Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2003-09-27 | YLR199C |
| Based on the alignment of orthologs in related Saccharomyces species, Cliften et al. 2003 proposed an intron and new 5' exon for YLR199C. The resulting ORF is in the same frame, but with the start moved upstream 254 bp. The old coding sequence was 663 nt long, and is now 831 nt long. This change was reviewed and accepted by SGD curators.Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2003-09-27 | YLR054C |
| Based on the alignment of orthologs in related fungi, Cliften et al. and Brachat et al. both proposed an intron and new 5' exon for YLR054C. The resulting ORF is in the same frame, but has a 212-residue extension at the N-terminus.Brachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2004-02-03 | YLR445W |
| Based on analyses of homology and synteny in Ashbya gossypii, Brachat et al. proposed an intron and 3' extension for YLR445W. The resulting ORF is in the same frame with the stop codon shifted 244 bp downstream; the protein has a 54-residue extension at the C-terminus.Brachat S, et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4(7):R45 | |
| 2004-10-12 | CEN12 |
| The orientation of this centromere was reversed (from Watson to Crick) to accommodate annotation of the centromeric DNA elements CDEI, CDEII, and CDEIII based on Wieland et al. and Espelin et al.Wieland G, et al. (2001) Determination of the binding constants of the centromere protein Cbf1 to all 16 centromere DNAs of Saccharomyces cerevisiae. Nucleic Acids Res 29(5):1054-60 Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68 | |
| 2005-11-17 | YLR146W-A |
| Based on genome sequence comparisons among six Saccharomyces species, Cliften et al. 2003 suggested that a new ORF, YLR146W-A, be added to the S. cerevisiae genome annotation.Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | |
| 2006-04-13 | ARS1208 |
| ARS1208, also known as "CEN12 ARS", was added to the genome annotation for Chromosome XII at coordinates 150946-151388 based on Wyrick et al. 2001 and Gammie & Rose 1995.Gammie AE and Rose MD (1995) Identification and characterization of CEN12 in the budding yeast Saccharomyces cerevisiae. Curr Genet 28(6):512-6 Wyrick JJ, et al. (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294(5550):2357-60 | |
| 2006-09-08 | ARS1206, ARS1209, ARS1211, ARS1212, ARS1213, ARS1215, ARS1216, ARS1217, ARS1218, ARS1220, ARS1223, ARS1226, ARS1232, ARS1233, ARS1234 |
| The following new ARS elements on Chromosome XII were added to SGD based on Nieduszynski et al. 2006: ARS1206, ARS1209, ARS1211, ARS1212, ARS1213, ARS1215, ARS1216, ARS1217, ARS1218, ARS1220, ARS1223, ARS1226, ARS1232, ARS1233, ARS1234.Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9 | |
| 2006-10-02 | ARS1238 |
| ARS1238, also known as ARS1227.5, was added to the genome annotation based on Nieduszynski et al. 2006.Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9 | |
| 2006-10-03 | YLR312W-A |
| Based on N-terminal sequencing by Kitakawa et al., the intron and first exon have been removed from the annotation of MRPL15/YLR312W-A. The newly annotated start codon is located 97 nt downstream of the originally annotated start, within what was previously annotated as intron sequence. Special Thanks to Ivo Pedruzzi and the team at Swiss-Prot for bringing this change to our attention.Kitakawa M, et al. (1997) Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae. Eur J Biochem 245(2):449-56 | |
| 2007-02-06 | ARS1200-1, ARS1200-2 |
| The rDNA ARS, as two copies ARS1200-1 and ARS1200-2, is being added to the genome annotation based on Miller & Kowalski 1993.Miller CA and Kowalski D (1993) cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol Cell Biol 13(9):5360-9 | |
| 2007-04-03 | YLRWdelta24 |
| YLRCdelta24, a Ty1 LTR on Chromosome XII, was mistakenly annotated on the wrong strand (i.e., on Crick instead of Watson). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YLRWdelta24 and is annotated on the Watson strand. The name YLRCdelta24 is being retained as an alias. | |
| 2007-04-04 | YLR333C |
| RPS25B/YLR333C mRNA contains an intron in the 5' untranslated region (UTR).Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51 Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7 | |
| 2007-04-04 | YLR367W |
| RPS22B/YLR367W mRNA contains an intron in the 5' untranslated region (UTR).Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51 | |
| 2007-04-04 | YLR388W |
| RPS29A/YLR388W mRNA contains an intron in the 5' untranslated region (UTR).Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 Miura F, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103(47):17846-51 Juneau K, et al. (2007) High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci U S A 104(5):1522-7 | |
| 2007-05-09 | snR30 |
| Updated coordinates of snR30 based on GenBank Z72300, Z73199. Moved 3' end downstream 5 nt. | |
| 2007-05-10 | snR34 |
| Updated coordinates of snR34 based on Samarsky et al. 1995 and GenBank L33802. Old coordinates were 898987..899536 (550 nt); new coordinates are 899180..899382 (203 nt).Samarsky DA, et al. (1995) Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35 and snR36. Nucleic Acids Res 23(13):2548-54 | |
| 2009-05-08 | ARS1202, ARS1207, ARS1214, ARS1219, ARS1221, ARS1228, ARS1230 |
| The following ARS elements on Chromosome 12 were added to the genome annotation based on Raveendranathan et al. 2006: ARS1202, ARS1207, ARS1214, ARS1219, ARS1221, ARS1228, and ARS1230.Raveendranathan M, et al. (2006) Genome-wide replication profiles of S-phase checkpoint mutants reveal fragile sites in yeast. EMBO J 25(15):3627-39 |
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