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Chromosome X History |
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| 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 |
|---|---|---|---|---|---|---|
| 2009-02-18 | YJL156C | 126896 | 126896 | Deletion | T | |
Poulsen et al. 2005 report an error in the systematic reference sequence for SSY5/YJL156C. There is an extra A in codon 685 (GAC) that should not be present in the sequence. SGD curators have corrected the sequence as necessary. Deletion of the A results in a frameshift that makes the Ssy5 protein 12 amino acids longer than previously annotated. Many thanks to Thorsten Pfirrmann for bringing this error to our attention.
new: 2113 TCAAAAAGGCAAATCATCCATCTAGTTGTGGATCAATGTCCCATTGAATTTTAGTTACAG 2054
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
old: 126836 TCAAAAAGGCAAATCATCCATCTAGTTGTGGATCAATGTCCCATTGAATTTTAGTTACAG 126895
new: 2053 -CATGTAGTCTCTCCAGGATATCACCTATAGGTGTGAACAAACCAAACTGCCTCTGTTCA 1995
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
old: 126896 TCATGTAGTCTCTCCAGGATATCACCTATAGGTGTGAACAAACCAAACTGCCTCTGTTCA 126955Poulsen P, et al. (2005) Constitutive Signal Transduction by Mutant Ssy5p and Ptr3p Components of the SPS Amino Acid Sensor System in Saccharomyces cerevisiae. Eukaryot Cell 4(6):1116-24   | ||||||
| 2008-06-04 | ||||||
| YJR092W | ||||||
| 599640 | 599640 | Deletion | A | |||
| 599597 | 599597 | Deletion | A | |||
| 599750 | 599750 | Substitution | A | T | ||
| 599715 | 599715 | Deletion | A | |||
John Koschwanez from Andrew Murray's lab at Harvard University sequenced BUD4/YJR092W in the S288C background and noted errors in the systematic reference sequence. As a result, the following corrections were made to the sequence of Chromosome 10 within BUD4/YJR092W: change A to T at 599750, delete A at 599715, delete A at 599640, delete A at 599597.
New: 841 AGTAACAATTCACATTCTGATTCAAGATC-GCCAACAGCCTCTGTGGAGGATTTAAACAT 899
||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Old: 599568 AGTAACAATTCACATTCTGATTCAAGATCAGCCAACAGCCTCTGTGGAGGATTTAAACAT 599627
New: 900 TTCAACGAATCT-GCCGGGTGCTGATTCCAGCCAAAATAATCCAGTCACTACTGATGCGG 958
|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
Old: 599628 TTCAACGAATCTAGCCGGGTGCTGATTCCAGCCAAAATAATCCAGTCACTACTGATGCGG 599687
New: 959 ATGCGCTTATTGAAAACGATGTTGTGC-GGGACCTTCAACAGAATATGGAACATATCGAT 1017
||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||
Old: 599688 ATGCGCTTATTGAAAACGATGTTGTGCAGGGACCTTCAACAGAATATGGAACATATCGAT 599747
New: 1018 GATGCTTTTGATGAGAAAAAAGTTCTTGACGAAGGTTGCAGCAATGAGCCCGTTACCTTT 1077
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old: 599748 GAAGCTTTTGATGAGAAAAAAGTTCTTGACGAAGGTTGCAGCAATGAGCCCGTTACCTTT 599807Koschwanez J and Murray A (2008)  | ||||||
| 2006-10-04 | YJL159W | 120806 | 120909 | Substitution | GTGATGGTCAAATTCAAGCTACCAC CAAGACTACCTCTGCTAAGACTACC GCCGCTGCCGTTTCTCAAATCAGTG ATGGTCAAATCCAAGCTACCACCAC TACT | AAATTGGTGATGGTCAAATTCAAGC TACCACCAAGACTACCTCTGCTAAG ACTACCGCCGCTGCCGTTTCTCAAA TCAGTGATGGTCAAATCCAAGCTAC CACCACTACTTTAGCCCCAAAGAGC ACCGCTGCTGCCGTTTCTCAAATCG GTGATGGTCAAGTTCAAGCTACCAC CACTACT |
Moukadiri and Zueco 2001 predicted, but did not confirm, two additional sequence insertions in HSP150/YJL159W. These two insertions (6 nts and 72 nts) were later confirmed in S288C by Marinangeli et al. 2004, and have been incorporated in SGD. Special thanks to Ivo Pedruzzi and the team at Swiss-Prot for bringing this change to our attention.
new 120745 TCTCAGATCGGTGATGGTCAAATCCAAGCTACTACTAAGACTACCGCTGCTGCTGTCTCT 120804
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
old 120745 TCTCAGATCGGTGATGGTCAAATCCAAGCTACTACTAAGACTACCGCTGCTGCTGTCTCT 120804
new 120805 CAAATTGGTGATGGTCAAATTCAAGCTACCACCAAGACTACCTCTGCTAAGACTACCGCC 120864
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
old 120805 C------GTGATGGTCAAATTCAAGCTACCACCAAGACTACCTCTGCTAAGACTACCGCC 120858
new 120865 GCTGCCGTTTCTCAAATCAGTGATGGTCAAATCCAAGCTACCACCACTACTTTAGCCCCA 120924
|||||||||||||||||||||||||||||||||||||||||||||||||||
old 120859 GCTGCCGTTTCTCAAATCAGTGATGGTCAAATCCAAGCTACCACCACTACT--------- 120909
new 120924 AAGAGCACCGCTGCTGCCGTTTCTCAAATCGGTGATGGTCAAGTTCAAGCTACCACCACT 120984
old ------------------------------------------------------------
new 120985 ACTTTAGCCCCAAAGAGCACCGCTGCTGCCGTTTCTCAAATCGGTGATGGTCAAGTTCAA 121044
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
old 120910 ---TTAGCCCCAAAGAGCACCGCTGCTGCCGTTTCTCAAATCGGTGATGGTCAAGTTCAA 120966
Moukadiri I and Zueco J (2001) YJL159w does encode Pir2/Hsp150. Yeast 18(4):323-4 Marinangeli P, et al. (2004) Minisatellites in Saccharomyces cerevisiae genes encoding cell wall proteins: a new way towards wine strain characterisation. FEMS Yeast Res 4(4-5):427-35 | ||||||
| 2006-01-18 | YJL170C | 101726 | 101726 | Insertion | G | |
SGD confirmed the sequence error suggested by Kellis et al and has updated the sequence accordingly. As a consequence of this change, ASG7/YJL170C has been extended on the 5' end, altering the N-terminus and increasing the size of the predicted protein from 183 to 209 amino acids.
Insert a G after the G at 101726
New: 101713 TCTCGAAGGGCGCGGCTAGATGTTTTGTTTT 101743
|||||||||||||| ||||||||||||||||
Old: 101713 TCTCGAAGGGCGCG-CTAGATGTTTTGTTTT 101742
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54  | ||||||
| 2006-01-18 | ||||||
| YJL162C | ||||||
| 114177 | 114177 | Substitution | T | A | ||
| 114328 | 114328 | Substitution | G | C | ||
SGD confirmed the sequence error suggested by Kellis et al and has updated the sequence accordingly. As a consequence of this change, JJJ2/YJL162C has been extended on the 3' end, altering the C-terminus and increasing the size of the predicted protein from 482 to 583 amino acids.
(1) Substitute A for the T at 114177
New: 114156 ATCTCTGGTATTTCCAAATCTAAGATCTCGGGTGTAAT 114193
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Old: 114156 ATCTCTGGTATTTCCAAATCTTAGATCTCGGGTGTAAT 114193
AND
(2) Substitute C for the G at 114328
New: 114311 TAACGAGTCATTAATTGCATCCATCATAAAATAATC 114346
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Old: 114311 TAACGAGTCATTAATTGGATCCATCATAAAATAATC 114346
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 | ||||||
| 2004-02-19 | YJL160C | 118303 | 118303 | Deletion | T | |
Kellis et al. and Brachat et al. independently predicted and confirmed the deletion of a single T nt. As a consequence of this sequence change, YJL160C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 180 to 287 amino acids.
New: 118271 CTTTTTCATTATTTGGTTTCTTTGTTGGCTCT-AACTTACTCTTGGAAAGCACAGAACTA 118329
|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Old: 118271 CTTTTTCATTATTTGGTTTCTTTGTTGGCTCTTAACTTACTCTTGGAAAGCACAGAACTA 118330 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 | ||||||
| 2004-02-18 | YJL159W | 121258 | 121258 | Insertion | CTACTTCCGCTTCTGCAGCCGCTAC CTCCACTGACCCAGTCGATGCTGTC TCCTGTAAGACTTCTGGTACCTTAG AAATGAACTTAAAGGGCGGTATCTT AACTGACGGTAAGGGTAGAATTGGT TCTATTGTTGCTAACAGACAATTCC AATTTGACGGTCCACCACCACAAGC TGGTGCCATCTACGCTGCTGGTTGG TCTATAACTCCAGACGGTAA | |
Both Brachat et al. 2003 and Moukadiri and Zueco 2001 independently predicted and confirmed a 220-bp insertion within HSP150/YJL159W. As a consequence of this sequence change, HSP150/YJL159W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 310 to 387 amino acids.
New: 121225 CAAGTAAGCGATGGCCAAGTCCAAGCTACTACTGCTACTTCCGCTTCTGCAGCCGCTACC 121284
||||||||||||||||||||||||||||||||||
Old: 121225 CAAGTAAGCGATGGCCAAGTCCAAGCTACTACTG-------------------------- 121258
New: 121285 TCCACTGACCCAGTCGATGCTGTCTCCTGTAAGACTTCTGGTACCTTAGAAATGAACTTA 121344
Old: ------------------------------------------------------------
New: 121345 AAGGGCGGTATCTTAACTGACGGTAAGGGTAGAATTGGTTCTATTGTTGCTAACAGACAA 121404
Old: ------------------------------------------------------------
New: 121405 TTCCAATTTGACGGTCCACCACCACAAGCTGGTGCCATCTACGCTGCTGGTTGGTCTATA 121464
Old: ------------------------------------------------------------
New: 121465 ACTCCAGACGGTAACTTGGCTATTGGTGACAATGATGTCTTCTACCAATGTTTGTCCGGT 121524
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Old: 121259 --------------CTTGGCTATTGGTGACAATGATGTCTTCTACCAATGTTTGTCCGGT 121304 Moukadiri I and Zueco J (2001) YJL159w does encode Pir2/Hsp150. Yeast 18(4):323-4 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 | ||||||
| 2004-02-17 | YJL012C, YJL012C-A | 411268 | 411268 | Insertion | C | |
Heinz Neumann and coworkers predicted and confirmed a single nt insertion in VTC4/YJL012C (Genbank accession number AY264259). As a consequence of this sequence change, VTC4/YJL012C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 648 to 721 amino acids. As a consequence of this change, YJL012C-A was merged with VTC4/YJL012C.
New: 411230 TTTTGGTTCCACACGAACTGGCACACATATCGTCTTTCCCGGTGGGGCACGAATTTGAGT 411289
||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Old: 411230 TTTTGGTTCCACACGAACTGGCACACATATCGTCTTTCC-GGTGGGGCACGAATTTGAGT 411288 Muller O, et al. (2003) Role of the Vtc proteins in V-ATPase stability and membrane trafficking. J Cell Sci 116(Pt 6):1107-15 | ||||||
| 2004-02-12 | YJL178C | 89893 | 89893 | Insertion | G | |
Brachat et al. predicted and confirmed the insertion of a single G nt. As a consequence of this sequence change, YJL178C was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 196 to 271 amino acids.
New: 89864 ATAGCATGTCATTTTTTTTACATTCTTCAGGAGGTTCTACGTTATGCTCTTCGCAAACGT 89923
|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Old: 89864 ATAGCATGTCATTTTTTTTACATTCTTCAG-AGGTTCTACGTTATGCTCTTCGCAAACGT 89922 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 | ||||||
| 2004-02-12 | YJR013W | 460195 | 460195 | Deletion | T | |
Brachat et al. predicted and confirmed the deletion of a single T nt. As a consequence of this sequence change, YJR013W was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 305 to 403 amino acids. This change was also predicted by
Cliften et al. and Kellis et al..
New: 460173 GTACACTGATATCGACTATTTT-GTGTTTCATGATGCTGCTAAATATGTATACGAAGGCA 460231
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Old: 460173 GTACACTGATATCGACTATTTTTGTGTTTCATGATGCTGCTAAATATGTATACGAAGGCA 460232 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 Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6 | ||||||
| 2003-09-29 | YJL016W, YJL017W | 406238 | 406238 | Insertion | G | |
| Due to insertion of G after the G at position 406238, the ORF YJL017W (405284-406261 (1-978)) was merged into YJL016W (406453-406968 (1-516)). The resulting longer ORF will retain the name YJL016W, with new coordinates 405284 - 406969 (1-1686). YJL017W is now an alias of YJL016W.
Old: 406201 TAGTGGATCCATCTATAGTAGTGCAAACAACGGCAGTG-TGACAGCAGCTCGACAGCATT 406259
|||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
New: 406201 TAGTGGATCCATCTATAGTAGTGCAAACAACGGCAGTGGTGACAGCAGCTCGACAGCATT 406260References: 1. Sequence verification in S288c strain at SGD 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 | ||||||
| 2003-01-02 | YJL018W, YJL019W | 404443 | 404443 | Insertion | G | |
| Due to the insertion of a single G nucleotide after the G at 404443 on chromosome 10, YJL018W and YJL019W have been merged into one single ORF - MPS3/YJL019W. Note that YJL018W and NEP98 are now aliases for this merged ORF. We thank Sue L. Jasperson and Mark Winey
for reporting this sequence error to SGD.
Old: 404401 CATATCTCTGAGGAAATTTATCATCAACGGAGTGACACCGCAG-ATTTGCAAATAATTGA 404459
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New: 404401 CATATCTCTGAGGAAATTTATCATCAACGGAGTGACACCGCAGGATTTGCAAATAATTGA 404460Jaspersen SL, et al. (2002) Mps3p is a novel component of the yeast spindle pole body that interacts with the yeast centrin homologue Cdc31p. J Cell Biol 159(6):945-56 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 | ||||||
| 2001-06-27 | ||||||
| YJL020C, YJL021C | ||||||
| 399914 | 399914 | Insertion | GG | |||
| 399923 | 399923 | Insertion | GG | |||
Sequence update from MIPS introduces two Gs after position 399914, then two more Gs after position 399923 on chromosome 10. Due to these 4 G insertions, the earlier ORFs YJL020C and YJL021C are now merged into one long ORF YJL020C of 1157 amino acids. Old: 399901 CTGGAGGTACTGGG--TACTGGG--TACTGAAGGTGCAGAGAGTGCTGGAGGTGCTGGAG 399956
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New: 399901 CTGGAGGTACTGGGGGTACTGGGGGTACTGAAGGTGCAGAGAGTGCTGGAGGTGCTGGAG 399960
References:
| ||||||
| 1997-07-27 | ||||||
| YJR092W | ||||||
| 601831 | 601831 | Substitution | A | G | ||
| 598745 | 598745 | Deletion | A | |||
| 598678 | 598678 | Deletion | G | |||
| 598510 | 598510 | Deletion | T | |||
Three separate single nucleotide deletions were made in the systematic sequence in the region upstream of the ORF BUD4/YJR092W. The T at 598510 was deleted, as was the G at 598678, and the A at 598745. In addition, a single nucleotide transition was made within BUD4/YJR092W. The A at 601831 was changed to a G.
New: 598501 ACGCAAAAT-GGTTCCGAAGATACACCACACAACTGGAAGCTTCCGCTGCAGGAAATAGG 598559
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Old: 598501 ACGCAAAATTGGTTCCGAAGATACACCACACAACTGGAAGCTTCCGCTGCAGGAAATAGG 598560
New: 598620 TAGAGGTCGATCACCTTCTAAGATGTCTACCATCTCAAATGAAAGCCTTAATTTGGG-TC 598678
||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Old: 598621 TAGAGGTCGATCACCTTCTAAGATGTCTACCATCTCAAATGAAAGCCTTAATTTGGGGTC 598680
New: 598739 AAAA-CTCTGTTGCCAACGGGGCACTTGGTCATGCCAATTCTCCCAAAGTGCTTAATAAT 598797
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Old: 598741 AAAAACTCTGTTGCCAACGGGGCACTTGGTCATGCCAATTCTCCCAAAGTGCTTAATAAT 598800
New: 601798 TTTGAATTGCCCATAGATTTTAAAGGAAAAGCCGAAACATCCTCCGCTTCTTCTGAAAGA 601857
|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Old: 601801 TTTGAATTGCCCATAGATTTTAAAGGAAAAACCGAAACATCCTCCGCTTCTTCTGAAAGA 601860 | ||||||
| 1997-07-27 | YJL084C | 275144 | 275145 | Substitution | CC | GG |
The two CC nucleotides at chromosomal coordinates 275144-275145 within the ORF YJL084C were changed to GG.
New: 275101 AAGTTCGTCTTCTATTAAAACTTGATTTAAATCTGTGAAAAAAGGATTATCGTGTCTTAT 275160
||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old: 275101 AAGTTCGTCTTCTATTAAAACTTGATTTAAATCTGTGAAAAAACCATTATCGTGTCTTAT 275160 | ||||||
| ANNOTATION CHANGES without sequence changes | Jump to: Sequence changes |
| Date | Affected Features |
|---|---|
| 2007-05-08 | snR3 |
| Updated coordinates of snR3 based on GenBank Z49627, Z49629, and K01089. Changed from 195 nt in length to 194 nt by removing 1 nt from the 5' end.Tollervey D, et al. (1983) A U4-like small nuclear RNA is dispensable in yeast. Cell 35(3 Pt 2):753-62 | |
| 2007-04-04 | YJL130C |
URA2/YJL130C mRNA contains an intron in the 5' untranslated region (UTR).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  Zhang Z, et al. (2007) Genome-wide identification of spliced introns using a tiling microarray. Genome Res 17(4):503-9 | |
| 2007-04-04 | YJRCdelta19 |
| YJLWdelta19, a Ty1 LTR on Chromosome X, was mistakenly annotated on the wrong strand (i.e., on Watson instead of Crick). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YJRCdelta19 and is annotated on the Crick strand. The name YJLWdelta19 is being retained as an alias. | |
| 2007-04-04 | YJRCdelta16 |
| YJLWdelta16, a Ty1 LTR on Chromosome X, was mistakenly annotated on the wrong strand (i.e., on Watson instead of Crick). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YJRCdelta16 and is annotated on the Crick strand. The name YJLWdelta16 is being retained as an alias. | |
| 2007-04-04 | YJRCdelta15 |
| YJLWdelta15, a Ty1 LTR on Chromosome X, was mistakenly annotated on the wrong strand (i.e., on Watson instead of Crick). Both the orientation and the feature name have been corrected, so that the LTR now has the systematic name YJRCdelta15 and is annotated on the Crick strand. The name YJLWdelta15 is being retained as an alias. | |
| 2006-09-07 | ARS1011, ARS1012, ARS1014, ARS1018, ARS1020, ARS1022, ARS1024 |
| The coordinates of the following ARS elements on Chromosome X were updated based on Nieduszynski et al. 2006: ARS1011, ARS1012, ARS1014, ARS1018, ARS1020, ARS1022, ARS1024.Nieduszynski CA, et al. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev 20(14):1874-9 | |
| 2006-05-09 | YJR003C |
| The proposal by Kellis et al. was re-examined in light of sequenc
e data from S. kudriavzevii (another sensu stricto strain published by Cliften e
t al.). The S. kudriavzevii sequence supported the start codon suggested by Kell
is et al., so the start site for YJR003C was moved 60 nt (20 codons) downstream.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 | |
| 2005-12-01 | YJL046W |
| The start site of YJL046W is being moved 126 bp downstream from 352176 to 352302 based on 5' SAGE data used by Zhang & Dietrich 2005 to study transcription start sites. The size of the predicted protein is reduced from 451 aa to 409 aa.Zhang Z and Dietrich FS (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res 33(9):2838-51 | |
| 2004-10-12 | CEN10 |
| The orientation of this centromere was reversed (from Watson to Crick) and its coordinates expanded to accommodate annotation of the centromeric DNA elements CDEI, CDEII, and CDEIII based on Wieland et al. (2001) and Espelin et al. (2003).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 | |
| 2004-04-20 | YJR092W |
| Based on the automated comparison of closely related Saccharomyces species by Kellis et al., the start site for BUD4/YJR092W was moved 384 nt upstream. Evidence supporting this change: 1) This is the predicted start methionine in S. paradoxus, S. mikatae, and S. bayanus orthologs; 2) Significant sequence conservation begins abruptly at this ATG. 3) Sanders and Herskowitz 1996 reported cloning and sequencing the BUD4 gene. Their sequence, GenBank accession number U41641, predicts a protein sequence beginning at the same place (starting with the peptide sequence MHDAE) as in the other three species and with a high level of similarity to them; 4) MIPS also annotates the protein sequence for this ORF as beginning at the earlier possible start site.Sanders SL and Herskowitz I (1996) The BUD4 protein of yeast, required for axial budding, is localized to the mother/BUD neck in a cell cycle-dependent manner. J Cell Biol 134(2):413-27 Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54 | |
| 2004-01-27 | YJL031C |
| Moved start 198 bp upstream, added an intron which was previously absent from the annotation. Encoded protein is 327 aa, as opposed to the previously annotated 290 aa.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 | |
| 2003-09-22 | YJL096W |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for MRPL49/YJL096W be moved 189 nt (63 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) Graack et al (1998) identify MRPL49/YJL096W as 16kDa protein, a size consistent with the proposed change.Graack HR and Wittmann-Liebold B (1998) Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J 329 ( Pt 3)():433-48 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 | YJR022W |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for LSM8/YJR022W be moved 57 nt (19 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.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 | YJL153C |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for INO1/YJL153C be moved 66 nt (22 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; 2) this N-terminus confirmed by sequencing of purified protein (Dean-Johnson M and Henry SA).Dean-Johnson M and Henry SA (1989) Biosynthesis of inositol in yeast. Primary structure of myo-inositol-1-phosphate synthase (EC 5.5.1.4) and functional analysis of its structural gene, the INO1 locus. J Biol Chem 264(2):1274-83 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 | YJL091C |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for GWT1/YJL091C be moved 24 nt (8 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.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 | YJR017C |
| Based on the automated comparison of closely related Saccharomyces species, Kellis et al. suggest that the start site for ESS1/YJR017C be moved 60 nt (20 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) This is the start site published by Hanes et al.Hanes SD, et al. (1989) Sequence and mutational analysis of ESS1, a gene essential for growth in Saccharomyces cerevisiae. Yeast 5(1):55-72 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 | |
| 2003-09-09 | TEL10L, TEL10L-TR, TEL10L-XC, TEL10L-XR, TEL10L-YP, TEL10R, TEL10R-TR, TEL10R-XC, TEL10R-XR |
| The chromosomal locations for TEL10L-XC, TEL10L-TR, TEL10L-XR, TEL10L, TEL10R-XC, TEL10R-XR, TEL10R-TR, TEL10L-YP and TEL10R were generously provided by Ed Louis and Dave Barton (University of Leicester, UK). | |
| 2003-07-29 | YJL127C-B, YJR005C-A, YJR112W-A |
| Thanks to Brachat et al. for providing the coordinates of the following Chromosome X ORFs: YJR005C-A, YJR112W-A and YJL127C-B.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 | YJL020W-A, YJL026C-A, YJL077W-A, YJL077W-B, YJL222W-A, YJL222W-B, YJL225W-A, YJR140W-A |
| Thanks to Kumar et al. for providing the coordinates of the following Chromosome X ORFs: YJL026C-A, YJL077W-B, YJL222W-B, YJL225W-A, YJR140W-A, YJL222W-A, YJL077W-A, and YJL020W-A.Kumar A, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20(1):58-63 | |
| 2003-07-29 | YJL047C-A, YJL133C-A, YJL136W-A |
| Thanks to MIPS for providing the coordinates of the following Chromosome X ORFs: YJL047C-A, YJL133C-A, and YJL136W-A. | |
| 2003-07-29 | YJR151W-A |
| Thanks to Kessler et al. for providing the coordinates for YJR151W-A.Kessler MM, et al. (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13(2):264-71 | |
| 2003-07-29 | YJL197C-A |
| Thanks to
Oshiro et al., Velculescu et al., and Basrai et al. for providing the coordinates of YJL197C-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 | |
| 2002-12-16 | ARS1001, ARS1002, ARS1003, ARS1004, ARS1005, ARS1006, ARS1007, ARS1008, ARS1009, ARS1010, ARS1011, ARS1012, ARS1013, ARS1014, ARS1015, ARS1016, ARS1017, ARS1018, ARS1019, ARS1020, ARS1022, ARS1023, ARS1024, ARS1025 |
| Coordinates courtesy of Dr. Oscar M. Aparicio, University of Southern California.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 | |
| 2002-11-19 | YJLWTy4-1, YJLWdelta2 |
| The YJLWdelta2 element was initially mistakenly annotated as a separate LTR, though its coordinates completely overlapped with the full length transposon YJLWTy4-1. Thus, YJLWdelta2 has been deleted from the database. | |
| 2001-05-16 | snR128, snR190 |
| 2. Personal communication: Dr. Eric Steinmetz Dept. of Biomolecular Chemistry University of Wisconsin 1300 University Ave. Madison, WI 53706 | |
| 2000-10-17 | ARS1021 |
| ARS1021 (aka ARS121) and ARS1501 were added to the genome annotation after personal communication from Shlomo Eisenberg. See Walker et al. 1991 for ARS1021 and Raychaudhuri et al. 1997 for ARS1501.Raychaudhuri S, et al. (1997) Functional analysis of a replication origin from Saccharomyces cerevisiae: identification of a new replication enhancer. Nucleic Acids Res 25(24):5057-64 Walker SS, et al. (1991) Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae. Nucleic Acids Res 19(22):6255-62 | |
| 2000-08-11 | YJL205C |
| Old name: YJL206C-A; new name: YJL205C-A; date: 11/1998; old coord: ChrX 50443 50139; SGDID: S0003742; Name changed due to nomenclature |
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