Take our Survey

Chromosome XII History Help



 

This page lists all sequence and annotation changes that have been made to the Chromosome XII systematic reference sequence since its intial release on 1996-07-31.


SEQUENCE CHANGES, including any resulting annotation changesJump to: Annotation changes

DateAffected FeaturesStart Coordinate
of Change
End Coordinate
of Change
Type of ChangeOld SequenceNew Sequence
2011-02-03YLL054C3290232902Insertion 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
                |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Old    32881    AATTGTGGATTGTTTAATTTTG-TGTGAACGAAAAGGACTTATCCCTTCCCATACCCCAT  32939

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR022C, YLR023C185062185062SubstitutionGA
 A single nucleotide substitutuion was made in the intergenic region between ORFs SDO1/YLR022C and IZH3/YLR023C.
New    185041   ATATATACAAGGCACTGAGCAGAACAATACACGCTAAGTTTTGTTCTTTCATGAGGTCAT  185100
                |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Old    185040   ATATATACAAGGCACTGAGCAGGACAATACACGCTAAGTTTTGTTCTTTCATGAGGTCAT  185099

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03
YLR023C, YLR024C
187394187394DeletionA
187423187423DeletionA
 Two separate single nucleotide deletions were made in the intergenic region between ORFs IZH3/YLR023C and UBR2/YLR024C.
New    187381   ACCTTATCCATCAA-CACTTTCTCCATTTCCTGCAGGGTAAAA-AGAAAAGTGAAGTCAC  187438
                |||||||||||||| |||||||||||||||||||||||||||| ||||||||||||||||
Old    187380   ACCTTATCCATCAAACACTTTCTCCATTTCCTGCAGGGTAAAAAAGAAAAGTGAAGTCAC  187439

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR024C192416192416SubstitutionCT
 A single nucleotide substitution was made within ORF UBR2/YLR024C. Note that the protein sequence was not changed.
New    192359   TCTTCTAAAGCCTTCGTTATTGAGATTGCATATTCAACCGGTGTATTCAAAATTCTTGTTATTGTAGATG  192428
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Old    192360   TCTTCTAAAGCCTTCGTTATTGAGATTGCATATTCAACCGGTGTATTCAAAATTCTCGTTATTGTAGATG  192429

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR024C, YLR025W193483193483SubstitutionAC
 A single nucleotide substitution was made in the intergenic region between ORFs UBR2/YLR024C and SNF7/YLR025W.
New    193439   ATTGAAAGTATGAATGCGTTGATTATTGGGTTTCTCCCCACAGCTGTACATTGACGATGC  193498
                ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Old    193440   ATTGAAAGTATGAATGCGTTGATTATTGGGTTTCTCCCCACAGATGTACATTGACGATGC  193499

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

1997-07-30YLR028C199680199680InsertionT
 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
            |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Old: 199649 CTTTACACCAGACTGCACAGCTCTATAAACGT-GTCTGGGAAGGGAAAGAACGCATCGGA 199707
Note that this ORF is on the Crick strand, which is complementary to the sequence shown above.
2011-02-03YLR034C210771210771SubstitutionAT
 A single nucleotide substitution was made within ORF SMF3/YLR034C. Note that the protein sequence was not changed.
New    210719   ATGAACAACCATCAACTTTCTATTTGCGGTAAAATAAATTAAAGGAGCGGATACGATTGGTAAAATTAAG  210788
                ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Old    210720   ATGAACAACCATCAACTTTCTATTTGCGGTAAAATAAATTAAAGGAGCGGAAACGATTGGTAAAATTAAG  210789

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR162W-A, YLR163C491154491154DeletionC
 A single nucleotide deletion was made in the intergenic region between ORFs RRT15/YLR162W-A and MAS1/YLR163C.
New    491099   TGAAGAGGTAGGTACATATTCATTGGCAGATATTCTACAATGCAATTATTATGA-CCAATCACACAGTAT  491167
                |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old    491100   TGAAGAGGTAGGTACATATTCATTGGCAGATATTCTACAATGCAATTATTATGACCCAATCACACAGTAT  491169

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2004-02-05
YLR205C
553548553548InsertionG
553633553633InsertionC
 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:        ACATAATAGTACGCCAGAATACCCTGTCTGTATATAAAGCCATGTCTCATGGCGATGGCC
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Old: 553498 ACATAATAGTACGCCAGAATACCCTGTCTGTATATAAAGCCATGTCTCATG-CGATGGCC 553556

New: CTGTTTGCTAGCGCCCCCACGTCAGTGGGTGAGGGTATGATTGTATTGCTACTGTCCTCC
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Old: 553617 CTGTTTGCTAGCGCCCC-ACGTCAGTGGGTGAGGGTATGATTGTATTGCTACTGTCCTCC 553675

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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2011-02-03YLR277C, YLR278C699963699963SubstitutionGA
 A single nucleotide substitution was made in the intergenic region between ORFs YSH1/YLR277C and YLR278C.
New    699948   AAAAAAAAAAAAAAGGAATGAGTTTGTACATACTATTATATTAATGTAGTATCACGTTAAAAAGCCGTAG  700017
                ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    699950   AAAAAAAAAAAAAGGGAATGAGTTTGTACATACTATTATATTAATGTAGTATCACGTTAAAAAGCCGTAG  700019

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR309C750224750224SubstitutionCT
 A single nucleotide substitution was made within ORF IMH1/YLR309C. Note that the protein sequence was not changed.
New    750178   TCACTAAATTGTTTAACTTGTTCCTCCAAGTAACTCACAGTTTTTTCCTTTTGTTTATAA  750237
                |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old    750180   TCACTAAATTGTTTAACTTGTTCCTCCAAGTAACTCACAGTTTTCTCCTTTTGTTTATAA  750239

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2001-06-12YLR312W-A759511759511InsertionC
 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
            ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
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
SGD Papers Entry  Pubmed Entry  DOI full text  

2004-02-04YLR312C-B, YLR313C760763760764DeletionCC
 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--TGCCATAGGA
|||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct: 760715 CTTGAACAATTTTGATTTAGAGGCTTGAACATCATTCAAAATGCCCTGCCTGCCATAGGA 760774

Roemer T, et al. (1998) The Spa2-related protein, Sph1p, is important for polarized growth in yeast. J Cell Sci 111 ( Pt 4)():479-94
SGD Papers Entry  Pubmed Entry  

2011-02-03YLR313C760764760764Insertion 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
                |||||||||||||||||||||||||  |||||||||||||||||||||||||||||||||
Old    760740   CTTGAACATCATTCAAAATGCCCTG--TGCCATAGGAAGAACAACCATTGATTTACTCTC  760797

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR314C762846762846SubstitutionAT
 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
                |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Old    762828   TGTAAAGTTTTTTCTTCTAGTTGTTTAGATATTGGATCGAACTCTTTGAAAACTGAATTATCTTGCTTAA  762897

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR318W767026767027SubstitutionTCCT
 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
                ||||||||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||||||||
Old    766978   AAATCGTGGGTAACAGATGTAACGAACCTCATCTGCCGCCCAAATGGGTCCAACGATCATCCTCATCATC  767047

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR346C, YLR347C822958822958Insertion G
 A single nucleotide insertion was made in the intergenic region between ORFs YLR346C and KAP95/YLR347C.
New    822948   TCAGCAGGTGCGGCTGTGCCTTTTCACTTTCAGCTAAGATGTTTGCAAGCAAGAATTAACAGATAAGCCG  823017
                ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    822948   TCAGCAGGTGC-GCTGTGCCTTTTCACTTTCAGCTAAGATGTTTGCAAGCAAGAATTAACAGATAAGCCG  823016

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR378C, YLR380W878171878171DeletionG
 A single nucleotide deletion was made in the intergenic region between ORFs SEC61/YLR378C and CSR1/YLR380W.
New    878158   AAATCTTGGCACTT-GTCACTTACGCTCCTTTAAACAAAATCAAACATACAAATATACGG  878216
                |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Old    878157   AAATCTTGGCACTTGGTCACTTACGCTCCTTTAAACAAAATCAAACATACAAATATACGG  878216

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2004-02-04YLR389C899751899751InsertionT
 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:        GCTCTTTGTTTTCCACTTGAGATTTCAAATGTAGAATCAACTTCGATGCGTTCTCGCTCA
||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 899741 GCTCTTTGTTT-CCACTTGAGATTTCAAATGTAGAATCAACTTCGATGCGTTCTCGCTCA 899799

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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2006-01-09YLR401C922648922648InsertionG
 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
            ||||||||||||||| ||||||||||||||||
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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2011-02-03YLR402W924691924691Insertion 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
               ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Old:  924657   TTAAGTCTCTTCATCCCGTGTACTATTACCCGACA-GTTTCTGCGGCATGTTCTGTGGAA  924715

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR407W933639933639Insertion 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
                |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Old    933596   AATGCAGGCTGGACGGAAACGAGAAAGTGGGCTAATGCTGCCAA-GGCATGCCATGACTG  933654

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR412C-A, YLR412W949230949230Insertion C
 A single nucleotide insertion was made in the intergenic region bewteen ORFs BER1/YLR412W and YLR412C-A.
New    949197   TCATTCACTACATAGTACTTTATAACTAAACTGTAACCTTTCAGGGCATCGTAACCTGAC  949256
                |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Old    949195   TCATTCACTACATAGTACTTTATAACTAAACTGTAA-CTTTCAGGGCATCGTAACCTGAC  949253

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR447C, YLR448W10286071028607Insertion G
 A single nucleotide insertion was made in the intergenic region between ORFs VMA6/YLR447C and RPL6B/YLR448W.
New    1028577  TAACCTGGACTTGCCGTGCTAAGTCGGCCTTCTAGGCTGCGCTTCCGTTCAGCATCGTTT  1028636
                |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Old    1028574  TAACCTGGACTTGCCGTGCTAAGTCGGCCTTCTA-GCTGCGCTTCCGTTCAGCATCGTTT  1028632

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR449W, YLR450W10325331032533DeletionG
 A single nucleotide deletion was made in the intergenic region between ORFs FPR4/YLR449W and HMG2/YLR450W.
New    1032527  GTTATAGTAA-GACACTTCAGTGAGAAATTAATCTGACTTACTTTTACTTAATTGTGTTCTTTCCAAATT  1032595
                |||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Old    1032523  GTTATAGTAAGGACACTTCAGTGAGAAATTAATCTGACTTACTTTTACTTAATTGTGTTCTTTCCAAATT  1032592

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2011-02-03YLR451W, YLR452C10387691038769DeletionC
 A single nucleotide deletion was made in the intergenic region between ORFs LEU3/YLR451W and SST2/YLR452C.
New    1038716  TTTTAATGAATGAATTTGCGTTCAATCCCAAGGTTTAAAGTCCTTTTCTTTTTTTG-CGTAATGTTTACT  1038784
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
Old    1038713  TTTTAATGAATGAATTTGCGTTCAATCCCAAGGTTTAAAGTCCTTTTCTTTTTTTGCCGTAATGTTTACT  1038782

Engel SR, et al. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda)
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

ANNOTATION CHANGES without sequence changesJump to: Sequence changes

Date Affected Features
2009-05-08ARS1202, 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
SGD Papers Entry  Pubmed Entry  DOI full text  PMC full text  

2007-05-10snR34
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2007-05-09snR30
 Updated coordinates of snR30 based on GenBank Z72300, Z73199. Moved 3' end downstream 5 nt.
2007-04-04YLR388W
 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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  
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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  
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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  yfgdb  

2007-04-04YLR367W
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  

2007-04-04YLR333C
 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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  
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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  Web Supplement  yfgdb  
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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  yfgdb  

2007-04-03YLRWdelta24
 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.
2007-02-06ARS1200-1, 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
SGD Papers Entry  Pubmed Entry  PMC full text  

2006-10-03YLR312W-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
SGD Papers Entry  Pubmed Entry  DOI full text  

2006-10-02ARS1238
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  

2006-09-08ARS1206, 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  

2006-04-13ARS1208
 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
SGD Papers Entry  Pubmed Entry  DOI full text  
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
SGD Papers Entry  Pubmed Entry  DOI full text  yfgdb  SGD Curated Comments & Errata

2005-11-17YLR146W-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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2004-10-12CEN12
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  
Espelin CW, et al. (2003) Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. Mol Biol Cell 14(11):4557-68
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2004-02-03YLR445W
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2003-09-27YLR054C
 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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-27YLR199C
 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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YLR012C
 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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YLR027C
 The start site for AAT2/YLR027C was moved 42 nt (14 codons) downstream based on automated comparison of closely related Saccharomyces species. 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
SGD Papers Entry  Pubmed Entry  PMC full text  
Kellis M, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-22YLR435W
 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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  SGD Curated Comments & Errata
Cliften P, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71-6
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  

2003-09-09TEL12L, 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).
2003-07-29YLL019W-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
SGD Papers Entry  Pubmed Entry  DOI full text  Web Supplement  yfgdb  SGD Curated Comments & Errata

2003-07-29YLL006W-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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2003-07-29YLR154W-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
SGD Papers Entry  Pubmed Entry  PMC full text  
Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51
SGD Papers Entry  Pubmed Entry  DOI full text  yfgdb  
Oshiro G, et al. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12(8):1210-20
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  Web Supplement  yfgdb  

2003-07-29YLR307C-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
SGD Papers Entry  Pubmed Entry  PMC full text  DOI full text  

2003-07-29YLR264C-A
 Thanks to MIPS for providing the coordinates of YLR264C-A.
2001-03-09snR79
 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
SGD Papers Entry  Pubmed Entry  PMC full text  

2000-08-11YLR337C
 Old name: YLR337W; new name: YLR337C; date: 2/10/2000; old coord: ChrXII; SGDID: Unknown; old change found in mips
2000-07-22YLR316C
 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.
2000-07-14YLR093C
 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.
2000-07-14YLR211C
 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.
1999-07-17YLR406C
 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.
1999-07-17YLR362W
 The start site of YLR362W was moved 63 nucleotides downstream.
1998-05-21YLL018C-A, YLR262C-A
 The following 27 ORFs were added to the genome annotation based on Velculescu et al. 1997: YBL091C-A, YBL107W-A, YCR018C-A, YCR102W-A, YDL130W-A, YDR034C-A, YDR034W-B, YDR363W-A, YDR525W-A, YER048W-A, YER091C-A, YER138W-A, YGR122C-A, YIR020W-B, YKL033W-A, YKL053C-A, YKL162C-A, YLL018C-A, YLR262C-A, YML081C-A, YMR046W-A, YMR158C-B, YMR194C-A, YNR032C-A, YOL013W-A, YOR298C-A, and YPR002C-A.

The coordinates of the tag sequences along the genome were determined and each tag was classified into one of these four categories: 1) class 1 - within an existing ORF, 2) class 2 - within 500 bp downstream of existing an ORF, 3) class 4 - opposite of an existing ORF, or 4) class 3 - none of the above. The regions between two existing ORFs which contained one or more unique class 3 tags (number 4) above) were examined for potential coding sequences in which the unique tag was located either within the coding sequence or 500bp downstream of this sequence. BLASTP analysis was then performed for each potential ORF meeting these criteria against the non-redundant (nr) NCBI dataset, and those with a P value exponent of -6 or less were analyzed further. The BLAST results were analyzed on an individual basis for each potential ORF meeting the above criteria. Those potential ORFs which exhibited reasonable homology to other proteins, and did not appear to be matched with other proteins based on homology to repetitive sequences alone, were identified and entered into SGD.

Velculescu VE, et al. (1997) Characterization of the yeast transcriptome. Cell 88(2):243-51
SGD Papers Entry  Pubmed Entry  DOI full text  yfgdb  

1997-07-30YLR390W-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.

Jump to: Sequence Changes | Annotation Changes without Sequence Changes