New & Noteworthy
Reference Genome Annotation Update R64.3
August 03, 2021
The S. cerevisiae strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3, which released on April 21, 2021. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.3.1 (relative to genome sequence release R64.2.1).
This annotation update included:
- 7 new ORFs: OTO1/YGR227C-A, YHR052C-B, YHR054C-B, YJR107C-A, YKL104W-A, YLR379W-A, YMR008C-A
- 5 new ncRNAs: GAL10-ncRNA, TBRT/XUT_2F-154, SUT169, PHO84 lncRNA, GAL4 lncRNA
- 2 new uORFs for ROK1/YGL171W
- 1 new recombination enhancer: RE
- 1 new LTR: YELWdelta27
- 3 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C, LTO1/YNL260C
- 1 ORF with shifted translation stop plus new intron: LDO45/YMR147W
- Changed feature_type (and SO_term) for non-transcribed spacers: NTS1-2, NTS2-1, NTS2-2
- New systematic nomenclature system for entire annotated complement of ncRNAs
R64.3 Annotation update details
| Chr | Feature | Description of change | Reference |
|---|---|---|---|
| II | YNCB0008W aka GAL10-ncRNA | New ncRNA antisense to GAL10coordinates 276805..280645 | Houseley et al 2008 PMID:19061643,Pinskaya et al 2009 PMID:19407817, Geisler et al 2012 PMID:22226051 |
| II | YNCB0014W aka TBRT/XUT_2F-154 | New ncRNA antisense to TAT1coordinates 376610..378633 | Awasthi et al 2020 PMID:32081726 |
| III | RE/RE301 | New recombination enhancercoordinates 29108..29809 | Wu and Haber 1996 PMID:8861911 |
| V | YELWdelta27 | New Ty1 LTRcoordinates 449274..449626 | Nene et al 2018 PMID:29320491 |
| V | HPA3/YEL066W | Moved translation start to Met19old coordinates: 26667..27206new coordinates: 26721..27206 | Sampath et al 2013 PMID:23775086 |
| VII | OTO1/YGR227C-A | New ORFcoordinates 949052..949225 Crick | Makanae et al 2015 PMID:25781884 |
| VII | ROK1/YGL171W | Two new uORFscoordinates uORF1: 182286..182407coordinates uORF2: 182291..182329 | Jeon and Kim 2010 PMID:20969870 |
| VIII | YHR052C-B | New ORFcoordinates: 212519..212692 Crick | He et al 2018 PMID:29897761 |
| VIII | YHR054C-B | New ORFcoordinates: 214517..214690 Crick | He et al 2018 PMID:29897761 |
| VIII | SUT169/YNCH0011W | New ncRNAcoordinates 378254..379237 | Xu et al 2009 PMID:19169243,Geisler et al 2012 PMID:22226051, Huber et al 2016 PMID:27292640, Bunina et al 2017 PMID:28977638 |
| X | YJR012C | Moved start to Met76old coordinates: 459795..460418 Cricknew coordinates: 459795..460193 Crick | Sadhu et al 2018 PMID:29632376 |
| X | YJR107C-A | New ORFcoordinates 628457..628693 Crick | Yagoub et al 2015 PMID:26554900, He et al 2018 PMID:29897761 |
| XI | YKL104W-A | New ORFcoordinates 245032..245286 | He et al 2018 PMID:29897761 |
| XII | YLR379W-A | New ORFcoordinates: 877444..877716 | Internal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462 |
| XII | NTS1-2, NTS2-1, NTS2-2 | Change feature_type/SO_term from SO:0001637 rRNA_gene to SO:0000183 non_transcribed_region | |
| XIII | LDO45/YMR147W | Shift stop to be same as LDO16/YMR148W, add intronold coordinates 559199..559870new coordinates 559199..559780, 560156..560812 | Eisenberg-Bord et al 2018 PMID:29187527 |
| XIII | YMR008C-A | New ORFcoordinates 283081..283548 Crick | Internal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462 |
| XIII | YNCM0001W aka PHO84 lncRNA | New ncRNAcoordinates: 23564..26578 | Camblong et al 2007 PMID:18022365 |
| XIV | LTO1/YNL260C | Move start to Met37old coordinates: 156859..157455 Cricknew coordinates: 156859..157347 Crick | Paul et al 2015 PMID:26182403 |
| XVI | YNCP0002W aka GAL4 lncRNA | New ncRNAcoordinates: 79562..82648 | Geisler et al 2012 PMID:22226051 |
New systematic nomenclature system for noncoding RNA genes
| Chr | Systematic_name | Gene_name | Alias | Feature_type | Coordinates | Strand |
|---|---|---|---|---|---|---|
| I | YNCA0001W | HRA1 | ncRNA gene | 99305..99868 | + | |
| I | YNCA0002W | TRN1 | tP(UGG)A, tRNA-Pro | tRNA gene | 139152..139254 | + |
| I | YNCA0003W | SNR18 | snR18 | snoRNA gene | 142367..142468 | + |
| I | YNCA0004W | TGA1 | tA(UGC)A, tRNA-Ala | tRNA gene | 166267..166339 | + |
| I | YNCA0005W | SUP56 | tL(CAA)A, tRNA-Leu | tRNA gene | 181141..181254 | + |
| I | YNCA0006C | tS(AGA)A, tRNA-Ser | tRNA gene | 182522..182603 | – | |
| II | YNCB0001W | tL(UAA)B1, tRNA-Leu | tRNA gene | 9583..9666 | + | |
| II | YNCB0002W | tF(GAA)B, tRNA-Phe | tRNA gene | 36398..36488 | + | |
| II | YNCB0003W | SNR56 | snR56 | snoRNA gene | 88190..88277 | + |
| II | YNCB0004W | tI(AAU)B, tRNA-Ile | tRNA gene | 197494..197567 | + | |
| II | YNCB0005C | tG(GCC)B, tRNA-Gly | tRNA gene | 197629..197699 | – | |
| II | YNCB0006W | tS(AGA)B, tRNA-Ser | tRNA gene | 227075..227156 | + | |
| II | YNCB0007W | tT(AGU)B, tRNA-Thr | tRNA gene | 266378..266450 | + | |
| II | YNCB0008W | GAL10-ncRNA | ncRNA gene | 276805..280645 | + | |
| II | YNCB0009C | SNR161 | snR161 | snoRNA gene | 307185..307345 | – |
| II | YNCB0010W | TLC1 | telomerase RNA gene | 307587..308887 | + | |
| II | YNCB0011C | tV(UAC)B, tRNA-Val | tRNA gene | 326792..326865 | – | |
| II | YNCB0012W | tL(UAA)B2, tRNA-Leu | tRNA gene | 347603..347686 | + | |
| II | YNCB0013W | tQ(UUG)B, tRNA-Gln | tRNA gene | 350827..350898 | + | |
| II | YNCB0014W | TBRT | XUT_2F-154 | ncRNA gene | 376610..378633 | + |
| II | YNCB0015W | tR(UCU)B, tRNA-Arg | tRNA gene | 405878..405949 | + | |
| II | YNCB0016W | tD(GUC)B, tRNA-Asp | tRNA gene | 405960..406031 | + | |
| II | YNCB0017C | tC(GCA)B, tRNA-Cys | tRNA gene | 643007..643078 | – | |
| II | YNCB0018W | tE(UUC)B, tRNA-Glu | tRNA gene | 645167..645238 | + | |
| II | YNCB0019C | LSR1 | snRNA gene | 680688..681862 | – | |
| III | YNCC0001C | tE(UUC)C, tRNA-Glu | tRNA gene | 82462..82533 | – | |
| III | YNCC0002W | SUP53 | tL(CAA)C, tRNA-Leu | tRNA gene | 90859..90972 | + |
| III | YNCC0003C | SNR43 | snR43 | snoRNA gene | 107504..107712 | – |
| III | YNCC0004C | SUF2 | tP(AGG)C, tRNA-Pro | tRNA gene | 123577..123648 | – |
| III | YNCC0005W | tN(GUU)C, tRNA-Asn | tRNA gene | 127716..127789 | + | |
| III | YNCC0006C | SNR33 | snR33 | snoRNA gene | 142364..142546 | – |
| III | YNCC0007C | SUF16 | tG(GCC)C, tRNA-Gly | tRNA gene | 142701..142771 | – |
| III | YNCC0008W | tM(CAU)C, tRNA-Met | tRNA gene | 149920..149991 | + | |
| III | YNCC0009C | tK(CUU)C, tRNA-Lys | tRNA gene | 151284..151356 | – | |
| III | YNCC0010C | tQ(UUG)C, tRNA-Gln | tRNA gene | 168301..168372 | – | |
| III | YNCC0011W | SNR65 | snR65 | snoRNA gene | 177183..177282 | + |
| III | YNCC0012C | SNR189 | snR189 | snoRNA gene | 178610..178798 | – |
| III | YNCC0013W | SUP61 | tS(CGA)C, tRNA-Ser | tRNA gene | 227942..228042 | + |
| III | YNCC0014W | tT(AGU)C, tRNA-Thr | tRNA gene | 295484..295556 | + | |
| IV | YNCD0001W | tG(GCC)D1, tRNA-Gly | tRNA gene | 83548..83618 | + | |
| IV | YNCD0002C | SNR63 | snR63 | snoRNA gene | 323217..323471 | – |
| IV | YNCD0003W | tK(UUU)D, tRNA-Lys | tRNA gene | 359577..359672 | + | |
| IV | YNCD0004W | tA(AGC)D, tRNA-Ala | tRNA gene | 410379..410451 | + | |
| IV | YNCD0005C | tT(AGU)D, tRNA-Thr | tRNA gene | 434264..434336 | – | |
| IV | YNCD0006W | tS(AGA)D1, tRNA-Ser | tRNA gene | 437772..437853 | + | |
| IV | YNCD0007C | tV(UAC)D, tRNA-Val | tRNA gene | 488797..488870 | – | |
| IV | YNCD0008W | tL(UAA)D, tRNA-Leu | tRNA gene | 519743..519826 | + | |
| IV | YNCD0009W | tQ(UUG)D1, tRNA-Gln | tRNA gene | 520972..521043 | + | |
| IV | YNCD0010C | SNR47 | snR47 | snoRNA gene | 541602..541700 | – |
| IV | YNCD0011W | tR(UCU)D, tRNA-Arg | tRNA gene | 568882..568953 | + | |
| IV | YNCD0012W | tD(GUC)D, tRNA-Asp | tRNA gene | 568964..569035 | + | |
| IV | YNCD0013C | tR(ACG)D, tRNA-Arg | tRNA gene | 619969..620041 | – | |
| IV | YNCD0014C | tQ(UUG)D2, tRNA-Gln | tRNA gene | 645153..645224 | – | |
| IV | YNCD0015C | tI(AAU)D, tRNA-Ile | tRNA gene | 668007..668080 | – | |
| IV | YNCD0016C | tQ(UUG)D3, tRNA-Gln | tRNA gene | 802731..802802 | – | |
| IV | YNCD0017W | tI(UAU)D, tRNA-Ile | tRNA gene | 884361..884493 | + | |
| IV | YNCD0018W | SUP2 | tY(GUA)D, tRNA-Tyr | tRNA gene | 946312..946400 | + |
| IV | YNCD0019C | tS(AGA)D2, tRNA-Ser | tRNA gene | 980974..981055 | – | |
| IV | YNCD0020W | tG(GCC)D2, tRNA-Gly | tRNA gene | 992832..992902 | + | |
| IV | YNCD0021C | tE(CUC)D, tRNA-Glu | tRNA gene | 1017207..1017278 | – | |
| IV | YNCD0022C | tV(CAC)D, tRNA-Val | tRNA gene | 1075472..1075544 | – | |
| IV | YNCD0023C | tF(GAA)D, tRNA-Phe | tRNA gene | 1095370..1095461 | – | |
| IV | YNCD0024C | tX(XXX)D | tRNA gene | 1150842..1150941 | – | |
| IV | YNCD0025W | EMT1 | tM(CAU)D, tRNA-Met | tRNA gene | 1175829..1175901 | + |
| IV | YNCD0026W | tK(CUU)D1, tRNA-Lys | tRNA gene | 1201750..1201822 | + | |
| IV | YNCD0027C | SUF3 | tG(CCC)D, tRNA-Gly | tRNA gene | 1257008..1257079 | – |
| IV | YNCD0028W | tS(AGA)D3, tRNA-Ser | tRNA gene | 1305630..1305712 | + | |
| IV | YNCD0029C | tK(CUU)D2, tRNA-Lys | tRNA gene | 1352466..1352538 | – | |
| IV | YNCD0030W | SNR13 | snR13 | snoRNA gene | 1402919..1403042 | + |
| IV | YNCD0031C | tL(CAA)D, tRNA-Leu | tRNA gene | 1461715..1461829 | – | |
| IV | YNCD0032C | SNR84 | snR84 | snoRNA gene | 1492477..1493026 | – |
| V | YNCE0001C | SNR80 | snR80 | snoRNA gene | 52150..52320 | – |
| V | YNCE0002W | SNR67 | snR67 | snoRNA gene | 61352..61433 | + |
| V | YNCE0003W | SNR53 | snR53 | snoRNA gene | 61699..61789 | + |
| V | YNCE0004C | tG(GCC)E, tRNA-Gly | tRNA gene | 61890..61960 | – | |
| V | YNCE0005W | tS(AGA)E, tRNA-Ser | tRNA gene | 86604..86685 | + | |
| V | YNCE0006W | IMT4 | tM(CAU)E, tRNA-Met | tRNA gene | 100133..100204 | + |
| V | YNCE0007C | RPR1 | ncRNA gene | 117667..118035 | – | |
| V | YNCE0008C | tQ(UUG)E2, tRNA-Gln | tRNA gene | 131082..131153 | – | |
| V | YNCE0009C | tK(CUU)E1, tRNA-Lys | tRNA gene | 135425..135497 | – | |
| V | YNCE0010W | tR(UCU)E, tRNA-Arg | tRNA gene | 138666..138737 | + | |
| V | YNCE0011C | SNR14 | snR14 | snRNA gene | 167427..167586 | – |
| V | YNCE0012W | tE(UUC)E1, tRNA-Glu | tRNA gene | 177099..177170 | + | |
| V | YNCE0013W | tH(GUG)E1, tRNA-His | tRNA gene | 207357..207428 | + | |
| V | YNCE0014W | tQ(UUG)E1, tRNA-Gln | tRNA gene | 250286..250357 | + | |
| V | YNCE0015C | SUP19 | tS(UGA)E, tRNA-Ser | tRNA gene | 288443..288524 | – |
| V | YNCE0016C | tA(UGC)E, tRNA-Ala | tRNA gene | 312023..312095 | – | |
| V | YNCE0017W | SRG1 | ncRNA gene | 322212..322762 | + | |
| V | YNCE0018W | tE(UUC)E2, tRNA-Glu | tRNA gene | 354934..355005 | + | |
| V | YNCE0019W | SNR4 | snR4 | snoRNA gene | 424698..424883 | + |
| V | YNCE0020C | SNR52 | snR52 | snoRNA gene | 431129..431220 | – |
| V | YNCE0021C | tH(GUG)E2, tRNA-His | tRNA gene | 434541..434612 | – | |
| V | YNCE0022C | tK(CUU)E2, tRNA-Lys | tRNA gene | 435752..435824 | – | |
| V | YNCE0023W | tV(AAC)E1, tRNA-Val | tRNA gene | 438700..438773 | + | |
| V | YNCE0024W | SCR1 | ncRNA gene | 441987..442508 | + | |
| V | YNCE0025C | tI(AAU)E1, tRNA-Ile | tRNA gene | 443202..443275 | – | |
| V | YNCE0026W | tV(AAC)E2, tRNA-Val | tRNA gene | 469457..469530 | + | |
| V | YNCE0027C | tE(UUC)E3, tRNA-Glu | tRNA gene | 487331..487402 | – | |
| V | YNCE0028C | tR(ACG)E, tRNA-Arg | tRNA gene | 492352..492424 | – | |
| V | YNCE0029C | tI(AAU)E2, tRNA-Ile | tRNA gene | 551285..551358 | – | |
| VI | YNCF0001C | RUF21 | ncRNA gene | 57815..58521 | – | |
| VI | YNCF0002W | SUF9 | tP(UGG)F, tRNA-Pro | tRNA gene | 101376..101478 | + |
| VI | YNCF0003C | RUF20 | ncRNA gene | 131061..131503 | – | |
| VI | YNCF0004C | tN(GUU)F, tRNA-Asn | tRNA gene | 137486..137559 | – | |
| VI | YNCF0005C | tF(GAA)F, tRNA-Phe | tRNA gene | 157916..158007 | – | |
| VI | YNCF0006W | SUF20 | tG(GCC)F1, tRNA-Gly | tRNA gene | 162228..162298 | + |
| VI | YNCF0007W | SUP11 | tY(GUA)F1, tRNA-Tyr | tRNA gene | 167437..167525 | + |
| VI | YNCF0008C | tG(GCC)F2, tRNA-Gly | tRNA gene | 180974..181044 | – | |
| VI | YNCF0009C | tS(GCU)F, tRNA-Ser | tRNA gene | 191513..191613 | – | |
| VI | YNCF0010C | RUF22 | ncRNA gene | 199299..199813 | – | |
| VI | YNCF0011C | tA(AGC)F, tRNA-Ala | tRNA gene | 204924..204996 | – | |
| VI | YNCF0012C | SUP6 | tY(GUA)F2, tRNA-Tyr | tRNA gene | 210619..210707 | – |
| VI | YNCF0013W | RUF23 | ncRNA gene | 221714..221967 | + | |
| VI | YNCF0014C | tK(CUU)F, tRNA-Lys | tRNA gene | 226688..226760 | – | |
| VII | YNCG0001C | RME3 | ncRNA gene | 33109..35013 | – | |
| VII | YNCG0002C | tV(AAC)G3, tRNA-Val | tRNA gene | 73829..73902 | – | |
| VII | YNCG0003C | tH(GUG)G1, tRNA-His | tRNA gene | 110625..110696 | – | |
| VII | YNCG0004W | tK(UUU)G1, tRNA-Lys | tRNA gene | 115488..115583 | + | |
| VII | YNCG0005W | tK(CUU)G1, tRNA-Lys | tRNA gene | 122269..122341 | + | |
| VII | YNCG0006C | RME2 | ncRNA gene | 141898..144120 | – | |
| VII | YNCG0007C | tK(CUU)G2, tRNA-Lys | tRNA gene | 185714..185786 | – | |
| VII | YNCG0008W | tL(CAA)G1, tRNA-Leu | tRNA gene | 205521..205634 | + | |
| VII | YNCG0009C | tW(CCA)G1, tRNA-Trp | tRNA gene | 287350..287455 | – | |
| VII | YNCG0010W | SNR82 | snR82 | snoRNA gene | 316788..317055 | + |
| VII | YNCG0011W | tH(GUG)G2, tRNA-His | tRNA gene | 319781..319852 | + | |
| VII | YNCG0012W | SOE1 | tE(UUC)G1, tRNA-Glu | tRNA gene | 328583..328654 | + |
| VII | YNCG0013W | SNR10 | snR10 | snoRNA gene | 345986..346230 | + |
| VII | YNCG0014C | SNR39 | snR39 | snoRNA gene | 365163..365251 | – |
| VII | YNCG0015C | SNR39B | snR39B | snoRNA gene | 366374..366469 | – |
| VII | YNCG0016C | tE(UUC)G2, tRNA-Glu | tRNA gene | 401527..401598 | – | |
| VII | YNCG0017W | tR(UCU)G1, tRNA-Arg | tRNA gene | 405470..405541 | + | |
| VII | YNCG0018C | tV(AAC)G1, tRNA-Val | tRNA gene | 412294..412367 | – | |
| VII | YNCG0019W | SUP54 | tL(CAA)G2, tRNA-Leu | tRNA gene | 423092..423205 | + |
| VII | YNCG0020C | tF(GAA)G, tRNA-Phe | tRNA gene | 440716..440807 | – | |
| VII | YNCG0021W | tD(GUC)G1, tRNA-Asp | tRNA gene | 531610..531681 | + | |
| VII | YNCG0022W | tE(UUC)G3, tRNA-Glu | tRNA gene | 541850..541921 | + | |
| VII | YNCG0023C | tD(GUC)G2, tRNA-Asp | tRNA gene | 544577..544648 | – | |
| VII | YNCG0024W | SNR46 | snR46 | snoRNA gene | 545370..545566 | + |
| VII | YNCG0025C | tS(AGA)G, tRNA-Ser | tRNA gene | 561662..561743 | – | |
| VII | YNCG0026W | SNR48 | snR48 | snoRNA gene | 609584..609696 | + |
| VII | YNCG0027W | tT(UGU)G1, tRNA-Thr | tRNA gene | 661749..661820 | + | |
| VII | YNCG0028W | tL(GAG)G, tRNA-Leu | tRNA gene | 700675..700756 | + | |
| VII | YNCG0029C | tK(UUU)G2, tRNA-Lys | tRNA gene | 700953..701048 | – | |
| VII | YNCG0030C | tC(GCA)G, tRNA-Cys | tRNA gene | 707108..707179 | – | |
| VII | YNCG0031W | tN(GUU)G, tRNA-Asn | tRNA gene | 731137..731210 | + | |
| VII | YNCG0032W | tR(UCU)G3, tRNA-Arg | tRNA gene | 736340..736411 | + | |
| VII | YNCG0033W | tI(AAU)G, tRNA-Ile | tRNA gene | 739122..739195 | + | |
| VII | YNCG0034W | tA(AGC)G, tRNA-Ala | tRNA gene | 774349..774421 | + | |
| VII | YNCG0035W | SUF4 | tG(UCC)G, tRNA-Gly | tRNA gene | 779616..779687 | + |
| VII | YNCG0036W | tA(UGC)G, tRNA-Ala | tRNA gene | 794417..794489 | + | |
| VII | YNCG0037W | tV(AAC)G2, tRNA-Val | tRNA gene | 823482..823555 | + | |
| VII | YNCG0038C | tR(UCU)G2, tRNA-Arg | tRNA gene | 828723..828794 | – | |
| VII | YNCG0039W | tG(GCC)G1, tRNA-Gly | tRNA gene | 845649..845719 | + | |
| VII | YNCG0040C | tL(CAA)G3, tRNA-Leu | tRNA gene | 857378..857491 | – | |
| VII | YNCG0041W | tK(CUU)G3, tRNA-Lys | tRNA gene | 876394..876466 | + | |
| VII | YNCG0042C | tW(CCA)G2, tRNA-Trp | tRNA gene | 878710..878815 | – | |
| VII | YNCG0043C | tG(GCC)G2, tRNA-Gly | tRNA gene | 930953..931023 | – | |
| VII | YNCG0044C | SNR7-L | snR7-L | snRNA gene | 939459..939672 | – |
| VII | YNCG0045C | SNR7-S | snR7-S | snRNA gene | 939494..939672 | – |
| VII | YNCG0046W | tT(UGU)G2, tRNA-Thr | tRNA gene | 1004216..1004287 | + | |
| VIII | YNCH0001W | tH(GUG)H, tRNA-His | tRNA gene | 62755..62826 | + | |
| VIII | YNCH0002C | tV(AAC)H, tRNA-Val | tRNA gene | 85298..85371 | – | |
| VIII | YNCH0003C | tT(AGU)H, tRNA-Thr | tRNA gene | 116107..116179 | – | |
| VIII | YNCH0004C | tS(AGA)H, tRNA-Ser | tRNA gene | 133026..133107 | – | |
| VIII | YNCH0005W | tQ(UUG)H, tRNA-Gln | tRNA gene | 134321..134392 | + | |
| VIII | YNCH0006C | tA(AGC)H, tRNA-Ala | tRNA gene | 146242..146314 | – | |
| VIII | YNCH0007W | RUF5-1 | ncRNA gene | 212409..213118 | + | |
| VIII | YNCH0008W | RUF5-2 | ncRNA gene | 214407..215116 | + | |
| VIII | YNCH0009C | tF(GAA)H1, tRNA-Phe | tRNA gene | 237848..237939 | – | |
| VIII | YNCH0010C | tF(GAA)H2, tRNA-Phe | tRNA gene | 358478..358569 | – | |
| VIII | YNCH0011W | SUT169 | ncRNA gene | 378254..379237 | + | |
| VIII | YNCH0012W | SNR32 | snR32 | snoRNA gene | 381540..381727 | + |
| VIII | YNCH0013C | SUF8 | tP(UGG)H, tRNA-Pro | tRNA gene | 388893..388995 | – |
| VIII | YNCH0014W | SNR71 | snR71 | snoRNA gene | 411228..411317 | + |
| VIII | YNCH0015W | tT(UGU)H, tRNA-Thr | tRNA gene | 466990..467061 | + | |
| VIII | YNCH0016C | tV(CAC)H, tRNA-Val | tRNA gene | 475706..475778 | – | |
| IX | YNCI0001W | SNR68 | snR68 | snoRNA gene | 97111..97246 | + |
| IX | YNCI0002W | tT(AGU)I1, tRNA-Thr | tRNA gene | 175031..175103 | + | |
| IX | YNCI0003C | tI(AAU)I1, tRNA-Ile | tRNA gene | 183440..183513 | – | |
| IX | YNCI0004W | tE(CUC)I, tRNA-Glu | tRNA gene | 197592..197663 | + | |
| IX | YNCI0005W | tI(AAU)I2, tRNA-Ile | tRNA gene | 210665..210738 | + | |
| IX | YNCI0006W | SUP17 | tS(UGA)I, tRNA-Ser | tRNA gene | 248850..248931 | + |
| IX | YNCI0007C | tK(CUU)I, tRNA-Lys | tRNA gene | 300228..300300 | – | |
| IX | YNCI0008C | tD(GUC)I1, tRNA-Asp | tRNA gene | 324303..324374 | – | |
| IX | YNCI0009W | tT(AGU)I2, tRNA-Thr | tRNA gene | 325748..325820 | + | |
| IX | YNCI0010C | tD(GUC)I2, tRNA-Asp | tRNA gene | 336349..336420 | – | |
| IX | YNCI0011W | tE(UUC)I, tRNA-Glu | tRNA gene | 370417..370488 | + | |
| IX | YNCI0012 | ICR1 | ncRNA gene | 393884..397082 | – | |
| IX | YNCI0013W | PWR1 | ncRNA gene | 395999..396939 | + | |
| X | YNCJ0001C | tT(AGU)J, tRNA-Thr | tRNA gene | 59100..59172 | – | |
| X | YNCJ0002C | tE(UUC)J, tRNA-Glu | tRNA gene | 115939..116010 | – | |
| X | YNCJ0003C | SNR128 | snR128 | snoRNA gene | 139566..139691 | – |
| X | YNCJ0004C | SNR190 | snR190 | snoRNA gene | 139761..139950 | – |
| X | YNCJ0005C | tA(AGC)J, tRNA-Ala | tRNA gene | 197313..197385 | – | |
| X | YNCJ0006W | tD(GUC)J1, tRNA-Asp | tRNA gene | 204735..204806 | + | |
| X | YNCJ0007C | SNR37 | snR37 | snoRNA gene | 228094..228479 | – |
| X | YNCJ0008W | tR(ACG)J, tRNA-Arg | tRNA gene | 233939..234011 | + | |
| X | YNCJ0009C | SNR60 | snR60 | snoRNA gene | 349130..349233 | – |
| X | YNCJ0010W | SUP7 | tY(GUA)J1, tRNA-Tyr | tRNA gene | 354244..354332 | + |
| X | YNCJ0011W | tR(UCU)J1, tRNA-Arg | tRNA gene | 355374..355445 | + | |
| X | YNCJ0012W | tD(GUC)J2, tRNA-Asp | tRNA gene | 355456..355527 | + | |
| X | YNCJ0013C | tD(GUC)J3, tRNA-Asp | tRNA gene | 374424..374495 | – | |
| X | YNCJ0014C | tR(UCU)J2, tRNA-Arg | tRNA gene | 374506..374577 | – | |
| X | YNCJ0015W | tV(AAC)J, tRNA-Val | tRNA gene | 378360..378433 | + | |
| X | YNCJ0016C | EMT5 | tM(CAU)J1, tRNA-Met | tRNA gene | 391043..391115 | – |
| X | YNCJ0017C | tG(GCC)J1, tRNA-Gly | tRNA gene | 396726..396796 | – | |
| X | YNCJ0018W | tK(CUU)J, tRNA-Lys | tRNA gene | 414966..415038 | + | |
| X | YNCJ0019C | tW(CCA)J, tRNA-Trp | tRNA gene | 415931..416036 | – | |
| X | YNCJ0020W | EMT3 | tM(CAU)J2, tRNA-Met | tRNA gene | 422937..423009 | + |
| X | YNCJ0021C | SUP51 | tL(UAA)J, tRNA-Leu | tRNA gene | 424432..424515 | – |
| X | YNCJ0022C | IMT3 | tM(CAU)J3, tRNA-Met | tRNA gene | 517813..517884 | – |
| X | YNCJ0023C | tS(AGA)J, tRNA-Ser | tRNA gene | 524012..524093 | – | |
| X | YNCJ0024W | SUF23 | tG(GCC)J2, tRNA-Gly | tRNA gene | 531828..531898 | + |
| X | YNCJ0025W | HSX1 | tR(CCU)J, tRNA-Arg | tRNA gene | 538555..538626 | + |
| X | YNCJ0026W | tD(GUC)J4, tRNA-Asp | tRNA gene | 541508..541579 | + | |
| X | YNCJ0027C | SUP4 | tY(GUA)J2, tRNA-Tyr | tRNA gene | 542956..543044 | – |
| X | YNCJ0028C | IRT1 | ncRNA gene | 605936..607424 | – | |
| X | YNCJ0029W | tL(UAG)J, tRNA-Leu | tRNA gene | 617919..618019 | + | |
| X | YNCJ0030W | SNR3 | snR3 | snoRNA gene | 663749..663942 | + |
| XI | YNCK0001W | SNR64 | snR64 | snoRNA gene | 38811..38911 | + |
| XI | YNCK0002C | TRT2 | tT(CGU)K, tRNA-Thr | tRNA gene | 46735..46806 | – |
| XI | YNCK0003W | tN(GUU)K, tRNA-Asn | tRNA gene | 74624..74697 | + | |
| XI | YNCK0004W | tL(UAA)K, tRNA-Leu | tRNA gene | 84208..84291 | + | |
| XI | YNCK0005C | tE(UUC)K, tRNA-Glu | tRNA gene | 141018..141089 | – | |
| XI | YNCK0006C | tR(UCU)K, tRNA-Arg | tRNA gene | 162487..162558 | – | |
| XI | YNCK0007W | tK(CUU)K, tRNA-Lys | tRNA gene | 202999..203071 | + | |
| XI | YNCK0008W | tA(AGC)K1, tRNA-Ala | tRNA gene | 219895..219967 | + | |
| XI | YNCK0009W | SNR38 | snR38 | snoRNA gene | 283185..283279 | + |
| XI | YNCK0010W | tW(CCA)K, tRNA-Trp | tRNA gene | 302918..303023 | + | |
| XI | YNCK0011C | tV(AAC)K1, tRNA-Val | tRNA gene | 308144..308217 | – | |
| XI | YNCK0012C | tH(GUG)K, tRNA-His | tRNA gene | 313401..313472 | – | |
| XI | YNCK0013W | SNR69 | snR69 | snoRNA gene | 364776..364876 | + |
| XI | YNCK0014W | tV(AAC)K2, tRNA-Val | tRNA gene | 379680..379753 | + | |
| XI | YNCK0015C | SNR87 | snR87 | snoRNA gene | 431030..431138 | – |
| XI | YNCK0016W | tL(CAA)K, tRNA-Leu | tRNA gene | 458557..458670 | + | |
| XI | YNCK0017W | tR(ACG)K, tRNA-Arg | tRNA gene | 490968..491040 | + | |
| XI | YNCK0018C | tD(GUC)K, tRNA-Asp | tRNA gene | 513332..513403 | – | |
| XI | YNCK0019W | tA(AGC)K2, tRNA-Ala | tRNA gene | 517988..518060 | + | |
| XI | YNCK0020C | SNR42 | snR42 | snoRNA gene | 559016..559366 | – |
| XI | YNCK0021W | tK(UUU)K, tRNA-Lys | tRNA gene | 578965..579060 | + | |
| XII | YNCL0001W | tP(UGG)L, tRNA-Pro | tRNA gene | 92548..92650 | + | |
| XII | YNCL0002C | tS(AGA)L, tRNA-Ser | tRNA gene | 167944..168025 | – | |
| XII | YNCL0003W | SNR30 | snR30 | snoRNA gene | 198784..199389 | + |
| XII | YNCL0004C | tA(UGC)L, tRNA-Ala | tRNA gene | 214883..214955 | – | |
| XII | YNCL0005C | SNR79 | snR79 | snoRNA gene | 348427..348510 | – |
| XII | YNCL0006W | SNR6 | snR6 | snRNA gene | 366235..366346 | + |
| XII | YNCL0007W | tR(ACG)L, tRNA-Arg | tRNA gene | 374355..374427 | + | |
| XII | YNCL0008W | tD(GUC)L1, tRNA-Asp | tRNA gene | 427132..427203 | + | |
| XII | YNCL0009C | tQ(UUG)L, tRNA-Gln | tRNA gene | 448650..448721 | – | |
| XII | YNCL0010C | RDN37-1 | rRNA gene | 451575..458432 | – | |
| XII | YNCL0011C | ETS2-1 | rRNA gene | 451575..451785 | – | |
| XII | YNCL0012C | RDN25-1 | rRNA gene | 451786..455181 | – | |
| XII | YNCL0013C | ITS2-1 | rRNA gene | 455182..455413 | – | |
| XII | YNCL0014C | RDN58-1 | rRNA gene | 455414..455571 | – | |
| XII | YNCL0015C | ITS1-1 | rRNA gene | 455572..455932 | – | |
| XII | YNCL0016C | RDN18-1 | rRNA gene | 455933..457732 | – | |
| XII | YNCL0017C | ETS1-1 | rRNA gene | 457733..458432 | – | |
| XII | YNCL0018W | RDN5-1 | rRNA gene | 459676..459796 | + | |
| XII | YNCL0019C | ETS2-2 | rRNA gene | 460712..460922 | – | |
| XII | YNCL0020C | RDN37-2 | rRNA gene | 460712..467569 | – | |
| XII | YNCL0021C | RDN25-2 | rRNA gene | 460923..464318 | – | |
| XII | YNCL0022C | ITS2-2 | rRNA gene | 464319..464550 | – | |
| XII | YNCL0023C | RDN58-2 | rRNA gene | 464551..464708 | – | |
| XII | YNCL0024C | ITS1-2 | rRNA gene | 464709..465069 | – | |
| XII | YNCL0025C | RDN18-2 | rRNA gene | 465070..466869 | – | |
| XII | YNCL0026C | ETS1-2 | rRNA gene | 466870..467569 | – | |
| XII | YNCL0027W | RDN5-2 | rRNA gene | 468813..468931 | + | |
| XII | YNCL0028W | RDN5-3 | rRNA gene | 472465..472583 | + | |
| XII | YNCL0029W | RDN5-4 | rRNA gene | 482045..482163 | + | |
| XII | YNCL0030W | RDN5-5 | rRNA gene | 485697..485815 | + | |
| XII | YNCL0031W | RDN5-6 | rRNA gene | 489349..489469 | + | |
| XII | YNCL0032C | tL(UAG)L1, tRNA-Leu | tRNA gene | 592519..592619 | – | |
| XII | YNCL0033C | tI(UAU)L, tRNA-Ile | tRNA gene | 605300..605432 | – | |
| XII | YNCL0034W | tL(CAA)L, tRNA-Leu | tRNA gene | 628383..628497 | + | |
| XII | YNCL0035C | tA(AGC)L, tRNA-Ala | tRNA gene | 656934..657006 | – | |
| XII | YNCL0036C | tV(AAC)L, tRNA-Val | tRNA gene | 687859..687932 | – | |
| XII | YNCL0037W | tL(UAG)L2, tRNA-Leu | tRNA gene | 732090..732190 | + | |
| XII | YNCL0038W | tI(AAU)L1, tRNA-Ile | tRNA gene | 734802..734875 | + | |
| XII | YNCL0039W | tX(XXX)L | tRNA gene | 784354..784453 | + | |
| XII | YNCL0040W | tD(GUC)L2, tRNA-Asp | tRNA gene | 793918..793989 | + | |
| XII | YNCL0041C | SNR61 | snR61 | snoRNA gene | 794486..794575 | – |
| XII | YNCL0042C | SNR55 | snR55 | snoRNA gene | 794697..794794 | – |
| XII | YNCL0043C | SNR57 | snR57 | snoRNA gene | 794937..795024 | – |
| XII | YNCL0044W | tE(UUC)L, tRNA-Glu | tRNA gene | 797178..797249 | + | |
| XII | YNCL0045W | TRR4 | tR(CCG)L, tRNA-Arg | tRNA gene | 818609..818680 | + |
| XII | YNCL0046W | SNR44 | snR44 | snoRNA gene | 856710..856920 | + |
| XII | YNCL0047W | tK(UUU)L, tRNA-Lys | tRNA gene | 875376..875471 | + | |
| XII | YNCL0048W | SNR34 | snR34 | snoRNA gene | 899180..899382 | + |
| XII | YNCL0049C | tL(UAA)L, tRNA-Leu | tRNA gene | 962972..963055 | – | |
| XII | YNCL0050C | tN(GUU)L, tRNA-Asn | tRNA gene | 975983..976056 | – | |
| XII | YNCL0051C | tI(AAU)L2, tRNA-Ile | tRNA gene | 1052071..1052144 | – | |
| XIII | YNCM0001W | PHO84 lncRNA | ncRNA gene | 23564..26578 | + | |
| XIII | YNCM0002C | SNR85 | snR85 | snoRNA gene | 67768..67938 | – |
| XIII | YNCM0003W | ZOD1 | ncRNA gene | 91970..92027 | + | |
| XIII | YNCM0004C | tR(UCU)M2, tRNA-Arg | tRNA gene | 131825..131896 | – | |
| XIII | YNCM0005C | SNR54 | snR54 | snoRNA gene | 163535..163620 | – |
| XIII | YNCM0006W | SUP5 | tY(GUA)M1, tRNA-Tyr | tRNA gene | 168795..168883 | + |
| XIII | YNCM0007C | tG(GCC)M, tRNA-Gly | tRNA gene | 183898..183968 | – | |
| XIII | YNCM0008C | SUF7 | tP(UGG)M, tRNA-Pro | tRNA gene | 196068..196170 | – |
| XIII | YNCM0009C | tS(AGA)M, tRNA-Ser | tRNA gene | 259158..259239 | – | |
| XIII | YNCM0010W | tE(UUC)M, tRNA-Glu | tRNA gene | 290801..290872 | + | |
| XIII | YNCM0011W | SNR78 | snR78 | snoRNA gene | 297278..297364 | + |
| XIII | YNCM0012W | SNR77 | snR77 | snoRNA gene | 297506..297593 | + |
| XIII | YNCM0013W | SNR76 | snR76 | snoRNA gene | 297725..297833 | + |
| XIII | YNCM0014W | SNR75 | snR75 | snoRNA gene | 297918..298006 | + |
| XIII | YNCM0015W | SNR74 | snR74 | snoRNA gene | 298138..298225 | + |
| XIII | YNCM0016W | SNR73 | snR73 | snoRNA gene | 298307..298412 | + |
| XIII | YNCM0017W | SNR72 | snR72 | snoRNA gene | 298554..298651 | + |
| XIII | YNCM0018C | tA(AGC)M1, tRNA-Ala | tRNA gene | 321147..321219 | – | |
| XIII | YNCM0019W | tF(GAA)M, tRNA-Phe | tRNA gene | 352280..352370 | + | |
| XIII | YNCM0020W | tH(GUG)M, tRNA-His | tRNA gene | 363064..363135 | + | |
| XIII | YNCM0021C | tV(AAC)M1, tRNA-Val | tRNA gene | 372445..372518 | – | |
| XIII | YNCM0022C | tW(CCA)M, tRNA-Trp | tRNA gene | 379303..379408 | – | |
| XIII | YNCM0023C | tV(AAC)M2, tRNA-Val | tRNA gene | 420588..420661 | – | |
| XIII | YNCM0024W | tD(GUC)M, tRNA-Asp | tRNA gene | 463554..463625 | + | |
| XIII | YNCM0025C | tK(CUU)M, tRNA-Lys | tRNA gene | 480621..480693 | – | |
| XIII | YNCM0026C | SNR24 | snR24 | snoRNA gene | 499984..500072 | – |
| XIII | YNCM0027W | tL(CAA)M, tRNA-Leu | tRNA gene | 504895..505008 | + | |
| XIII | YNCM0028C | EMT4 | tM(CAU)M, tRNA-Met | tRNA gene | 572883..572955 | – |
| XIII | YNCM0029C | tV(AAC)M3, tRNA-Val | tRNA gene | 586636..586709 | – | |
| XIII | YNCM0030W | SNR83 | snR83 | snoRNA gene | 626349..626654 | + |
| XIII | YNCM0031W | SNR11 | snR11 | snoRNA gene | 652275..652532 | + |
| XIII | YNCM0032C | RNA170 | ncRNA gene | 667288..667456 | – | |
| XIII | YNCM0033C | tR(UCU)M1, tRNA-Arg | tRNA gene | 747892..747963 | – | |
| XIII | YNCM0034C | SNR86 | snR86 | snoRNA gene | 762110..763113 | – |
| XIII | YNCM0035C | tA(AGC)M2, tRNA-Ala | tRNA gene | 768369..768441 | – | |
| XIII | YNCM0036C | CDC65 | tQ(CUG)M, tRNA-Gln | tRNA gene | 808246..808317 | – |
| XIII | YNCM0037W | SUP8 | tY(GUA)M2, tRNA-Tyr | tRNA gene | 837928..838016 | + |
| XIV | YNCN0001W | SNR40 | snR40 | snoRNA gene | 89210..89306 | + |
| XIV | YNCN0002C | SUF6 | tG(UCC)N, tRNA-Gly | tRNA gene | 96241..96312 | – |
| XIV | YNCN0003W | tN(GUU)N1, tRNA-Asn | tRNA gene | 102716..102789 | + | |
| XIV | YNCN0004W | tT(AGU)N1, tRNA-Thr | tRNA gene | 104805..104877 | + | |
| XIV | YNCN0005C | SNR19 | snR19 | snRNA gene | 230105..230672 | – |
| XIV | YNCN0006W | tF(GAA)N, tRNA-Phe | tRNA gene | 374869..374959 | + | |
| XIV | YNCN0007W | tL(CAA)N, tRNA-Leu | tRNA gene | 443006..443119 | + | |
| XIV | YNCN0008C | tD(GUC)N, tRNA-Asp | tRNA gene | 519099..519169 | – | |
| XIV | YNCN0009W | tP(UGG)N1, tRNA-Pro | tRNA gene | 547094..547196 | + | |
| XIV | YNCN0010C | tT(AGU)N2, tRNA-Thr | tRNA gene | 560693..560765 | – | |
| XIV | YNCN0011W | tP(UGG)N2, tRNA-Pro | tRNA gene | 568115..568217 | + | |
| XIV | YNCN0012C | tI(AAU)N1, tRNA-Ile | tRNA gene | 569867..569940 | – | |
| XIV | YNCN0013W | NME1 | snoRNA gene | 585587..585926 | + | |
| XIV | YNCN0014W | SNR66 | snR66 | snoRNA gene | 586090..586175 | + |
| XIV | YNCN0015W | tI(AAU)N2, tRNA-Ile | tRNA gene | 602312..602385 | + | |
| XIV | YNCN0016C | SUF10 | tP(AGG)N, tRNA-Pro | tRNA gene | 631846..631917 | – |
| XIV | YNCN0017W | tN(GUU)N2, tRNA-Asn | tRNA gene | 632599..632672 | + | |
| XIV | YNCN0018W | SNR49 | snR49 | snoRNA gene | 716120..716284 | + |
| XIV | YNCN0019C | SNR191 | snR191 | snoRNA gene | 721938..722211 | – |
| XIV | YNCN0020C | tL(UAA)N, tRNA-Leu | tRNA gene | 726134..726217 | – | |
| XV | YNCO0001C | SUF1 | tG(UCC)O, tRNA-Gly | tRNA gene | 110962..111033 | – |
| XV | YNCO0002W | tT(AGU)O1, tRNA-Thr | tRNA gene | 113802..113874 | + | |
| XV | YNCO0003C | SNR58 | snR58 | snoRNA gene | 136088..136183 | – |
| XV | YNCO0004C | tG(GCC)O1, tRNA-Gly | tRNA gene | 226611..226681 | – | |
| XV | YNCO0005W | tN(GUU)O1, tRNA-Asn | tRNA gene | 228331..228404 | + | |
| XV | YNCO0006W | SNR81 | snR81 | snoRNA gene | 234346..234546 | + |
| XV | YNCO0007W | SNR50 | snR50 | snoRNA gene | 259489..259578 | + |
| XV | YNCO0008W | tS(GCU)O, tRNA-Ser | tRNA gene | 274673..274773 | + | |
| XV | YNCO0009W | SUF17 | tG(GCC)O2, tRNA-Gly | tRNA gene | 282164..282234 | + |
| XV | YNCO0010W | SUP3 | tY(GUA)O, tRNA-Tyr | tRNA gene | 288192..288280 | + |
| XV | YNCO0011W | tP(UGG)O1, tRNA-Pro | tRNA gene | 301097..301198 | + | |
| XV | YNCO0012C | tR(ACG)O, tRNA-ARg | tRNA gene | 340299..340371 | – | |
| XV | YNCO0013C | tT(AGU)O2, tRNA-Thr | tRNA gene | 354041..354113 | – | |
| XV | YNCO0014C | SNR9 | snR9 | snoRNA gene | 407948..408134 | – |
| XV | YNCO0015C | SNR62 | snR62 | snoRNA gene | 409765..409864 | – |
| XV | YNCO0016W | tK(UUU)O, tRNA-Lys | tRNA gene | 438643..438738 | + | |
| XV | YNCO0017W | SUF11 | tP(UGG)O2, tRNA-Pro | tRNA gene | 464450..464551 | + |
| XV | YNCO0018W | tN(GUU)O2, tRNA-Asn | tRNA gene | 487439..487512 | + | |
| XV | YNCO0019W | tD(GUC)O, tRNA-Asp | tRNA gene | 571958..572029 | + | |
| XV | YNCO0020C | SUF5 | tG(CCC)O | tRNA gene | 594354..594425 | – |
| XV | YNCO0021C | tV(AAC)O | tRNA gene | 663812..663885 | – | |
| XV | YNCO0022C | SNR36 | snR36 | snoRNA gene | 680685..680866 | – |
| XV | YNCO0023W | IMT1 | tM(CAU)O1, tRNA-Met | tRNA gene | 710201..710272 | + |
| XV | YNCO0024C | SNR35 | snR35 | snoRNA gene | 759326..759529 | – |
| XV | YNCO0025W | SNR17A | snR17a | snoRNA gene | 780107..780596 | + |
| XV | YNCO0026W | SNR8 | snR8 | snoRNA gene | 832332..832521 | + |
| XV | YNCO0027C | SNR31 | snR31 | snoRNA gene | 841958..842182 | – |
| XV | YNCO0028W | SNR5 | snR5 | snoRNA gene | 842403..842606 | + |
| XV | YNCO0029C | tA(UGC)O, tRNA-Ala | tRNA gene | 854187..854259 | – | |
| XV | YNCO0030W | EMT2 | tM(CAU)O2, tRNA-Met | tRNA gene | 976421..976493 | + |
| XV | YNCO0031W | tP(UGG)O3, tRNA-Pro | tRNA gene | 980683..980787 | + | |
| XVI | YNCP0001C | tW(CCA)P, tRNA-Trp | tRNA gene | 56169..56274 | – | |
| XVI | YNCP0002W | GAL4 lncRNA | ncRNA gene | 79562..82648 | + | |
| XVI | YNCP0003W | SNR59 | snR59 | snoRNA gene | 173827..173904 | + |
| XVI | YNCP0004C | tE(UUC)P, tRNA-Glu | tRNA gene | 210192..210263 | – | |
| XVI | YNCP0005C | SNR17B | snR17b | snoRNA gene | 281056..281517 | – |
| XVI | YNCP0006C | IMT2 | tM(CAU)P, tRNA-Met | tRNA gene | 338848..338919 | – |
| XVI | YNCP0007C | tC(GCA)P1, tRNA-Cys | tRNA gene | 435893..435964 | – | |
| XVI | YNCP0008C | tF(GAA)P1, tRNA-Phe | tRNA gene | 560198..560289 | – | |
| XVI | YNCP0009W | tG(GCC)P1, tRNA-Gly | tRNA gene | 572269..572339 | + | |
| XVI | YNCP0010W | tK(CUU)P, tRNA-Lys | tRNA gene | 582062..582134 | + | |
| XVI | YNCP0011C | tF(GAA)P2, tRNA-Phe | tRNA gene | 622540..622631 | – | |
| XVI | YNCP0012W | SUP16 | tS(UGA)P, tRNA-Ser | tRNA gene | 689565..689646 | + |
| XVI | YNCP0013C | SNR51 | snR51 | snoRNA gene | 718700..718806 | – |
| XVI | YNCP0014C | SNR70 | snR70 | snoRNA gene | 718887..719050 | – |
| XVI | YNCP0015C | SNR41 | snR41 | snoRNA gene | 719148..719242 | – |
| XVI | YNCP0016W | tT(UGU)P, tRNA-Thr | tRNA gene | 744284..744355 | + | |
| XVI | YNCP0017C | tK(UUU)P, tRNA-Lys | tRNA gene | 769207..769302 | – | |
| XVI | YNCP0018C | tC(GCA)P2, tRNA-Cys | tRNA gene | 775765..775836 | – | |
| XVI | YNCP0019W | tN(GUU)P, tRNA-Asn | tRNA gene | 810676..810749 | + | |
| XVI | YNCP0020W | tI(AAU)P1, tRNA-Ile | tRNA gene | 819529..819602 | + | |
| XVI | YNCP0021W | SNR45 | snR45 | snoRNA gene | 821732..821903 | + |
| XVI | YNCP0022W | tA(AGC)P, tRNA-Ala | tRNA gene | 856902..856974 | + | |
| XVI | YNCP0023W | tG(GCC)P2, tRNA-Gly | tRNA gene | 860379..860449 | + | |
| XVI | YNCP0024C | tI(AAU)P2, tRNA-Ile | tRNA gene | 880296..880369 | – | |
| Mito | YNCQ0001W | tP(UGG)Q, tRNA-Pro | tRNA gene | 731..802 | + | |
| Mito | YNCQ0002W | 15S_RRNA | Q0020 | rRNA gene | 6546..8194 | + |
| Mito | YNCQ0003W | tW(UCA)Q, tRNA-Trp | tRNA gene | 9374..9447 | + | |
| Mito | YNCQ0004W | tE(UUC)Q, tRNA-Glu | tRNA gene | 35373..35444 | + | |
| Mito | YNCQ0005W | tS(UGA)Q2, tRNA-Ser | tRNA gene | 48201..48290 | + | |
| Mito | YNCQ0006W | 21S_RRNA | Q0158 | rRNA gene | 58009..62447 | + |
| Mito | YNCQ0007W | tT(UGU)Q1, tRNA-Thr | tRNA gene | 63862..63937 | + | |
| Mito | YNCQ0008W | tC(GCA)Q, tRNA-Cys | tRNA gene | 64415..64490 | + | |
| Mito | YNCQ0009W | tH(GUG)Q, tRNA-His | tRNA gene | 64596..64670 | + | |
| Mito | YNCQ0010W | tL(UAA)Q, tRNA-Leu | tRNA gene | 66095..66179 | + | |
| Mito | YNCQ0011W | tQ(UUG)Q, tRNA-Gln | tRNA gene | 66210..66285 | + | |
| Mito | YNCQ0012W | tK(UUU)Q, tRNA-Lys | tRNA gene | 67061..67134 | + | |
| Mito | YNCQ0013W | tR(UCU)Q1, tRNA-Arg | tRNA gene | 67309..67381 | + | |
| Mito | YNCQ0014W | tG(UCC)Q, tRNA-Gly | tRNA gene | 67468..67542 | + | |
| Mito | YNCQ0015W | tD(GUC)Q, tRNA-Asp | tRNA gene | 68322..68396 | + | |
| Mito | YNCQ0016W | tS(GCU)Q1, tRNA-Ser | tRNA gene | 69203..69288 | + | |
| Mito | YNCQ0017W | tR(ACG)Q2, tRNA-Arg | tRNA gene | 69289..69362 | + | |
| Mito | YNCQ0018W | tA(UGC)Q, tRNA-Ala | tRNA gene | 69846..69921 | + | |
| Mito | YNCQ0019W | tI(GAU)Q, tRNA-Ile | tRNA gene | 70162..70237 | + | |
| Mito | YNCQ0020W | tY(GUA)Q, tRNA-Tyr | tRNA gene | 70824..70907 | + | |
| Mito | YNCQ0021W | tN(GUU)Q, tRNA-Asn | tRNA gene | 71433..71503 | + | |
| Mito | YNCQ0022W | tM(CAU)Q1, tRNA-Met | tRNA gene | 72630..72705 | + | |
| Mito | YNCQ0023W | tF(GAA)Q, tRNA-Phe | tRNA gene | 77431..77505 | + | |
| Mito | YNCQ0024C | tT(UAG)Q2, tRNA-Thr | tRNA gene | 78089..78162 | – | |
| Mito | YNCQ0025W | tV(UAC)Q, tRNA-Val | tRNA gene | 78533..78608 | + | |
| Mito | YNCQ0026W | tM(CAU)Q2, tRNA-Met | tRNA gene | 85035..85112 | + | |
| Mito | YNCQ0027W | RPM1 | Q0285 | ncRNA gene | 85295..85777 | + |
Various sequence and annotation files are available on SGD’s Downloads site.
Categories: Data updates
SGD Homology Data Now Available On New Homology Pages
March 25, 2021
SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.
The information displayed on the Homology Pages is divided into several sections:
- Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
- Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
- Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
- External Identifiers: A list of external identifiers for the protein from various database sources.
If you have any questions or feedback regarding our new Homology Pages, please do not hesitate to contact us at any time.
Categories: Data updates, Homologs, New Data, Yeast and Human Disease
Interactions Page Updates
November 06, 2020
SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page.
Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016).
Please be sure to watch our Interactions Page Updates tutorial video for a quick walk-through of the changes:
If you have any questions or feedback about the updates to our Interactions Pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates
Browse Metabolic Pathways at SGD
August 02, 2019
Did you know that SGD has over 200 curated biochemical pathways for you to explore? SGD’s YeastPathways is a database of metabolic pathways and enzymes in Saccharomyces cerevisiae. YeastPathways enables you to visualize yeast metabolism from large metabolic networks to individual pathways, and from biochemical reactions down to individual metabolites. Search tools and click-to-browse features in YeastPathways enable quick navigation and intuitive exploration of yeast metabolism.
As the first major content update to YeastPathways since 2012, we have recently updated 62 pathways with expertly-curated summaries on pathway biochemistry, genetics, regulation, and more. Compounds that were previously missing a structure have also now been updated, along with the stoichiometry and scheme of many pathway reactions. In addition to content updates, YeastPathways has also received a major software upgrade that provides new tools, pages, and visual aids.
With new content and software, YeastPathways is better than ever. Users new to YeastPathways will find that it’s easy to get started—simply access YeastPathways through the Function menu at SGD, then run a search for a pathway, compound, enzyme, or reaction on the YeastPathways homepage. You can also access YeastPathways through gene pages at SGD. Just run a search for your favorite metabolic enzyme at SGD (example: TPI1) and find the Pathways section on the locus summary page. Any pathways in which the protein is involved will be listed and linked to YeastPathways.
Check out YeastPathways and be sure to contact us if you have any questions or feedback!
Categories: Data updates
SK1 Sequence Updated in SGD
November 20, 2018
The alternative reference strain SK1 is a rapid and synchronously sporulating diploid constructed by Kane and Roth in the early 1970’s to study carbohydrate metabolism under sporulation conditions. Whereas the reference strain S288C is notorious for being poor at sporulation, SK1 undergoes sporulation readily, and as such has been widely used to study the genetics of sporulation and meiosis.
The genome of SK1, which was temporarily removed from SGD, is now available once again with an updated sequence provided by Scott Keeney from the Sloan Kettering Institute. You can access the updated SK1 sequence for your favorite genes from the Sequence tab, in the Alternative Reference Strains section (example: ECM22 Sequence page). To access the entire SK1 genome sequence, visit the SK1 Strain page.
In addition, we have updated following Sequence and Analysis tools to utilize the latest SK1 sequence:
Variant Viewer will be updated in a future release. Be sure to check out these updated tools and resources and let us know if you have any questions or comments.
Categories: Data updates, Website changes
Updated Genome Browser
March 27, 2016
In an effort to provide a comprehensive view of sequence-based functional elements in Saccharomyces cerevisiae, we have upgraded our genome browser, and added new data tracks, to allow users to quickly and easily browse the information-rich yeast genome. We invite authors to work with us to integrate published data into our new JBrowse genome viewer pre- and/or post-publication. Please contact us if you are interested in participating or have questions and comments. Watch for the regular addition of new tracks to SGD’s JBrowse in the future!
Take a look at our newest video tutorial to get acquainted with JBrowse, and let us know if you have any questions or suggestions.
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Data updates, Website changes
Reference Genome Annotation Update R64.2.1
February 23, 2015
SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C. Last November, the genome annotation was updated for the first time since the release of the major S288C resequencing update in February 2011. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.2.1 (relative to genome sequence release R64.1.1).
The R64.2.1 annotation release included various updates and additions. The annotations of 2 existing proteins changed (GRX3/YDR098C and HOP2/YGL033W), and 1 new ORF (RDT1/YCL054W-A) and 4 RNAs (RME2, RME3, IRT1, ZOD1) were added to the genome annotation. Other additions include 8 nuclear matrix attachment sites, and 8 mitochondrial origins of replication. The coordinates of many autonomously replicating sequences (ARS) were updated, and many new ARS consensus sequences were added. Complete details can be found in the Summary of Chromosome Sequence and Annotation Updates.
Categories: Data updates, New Data, Sequence
New Protein Modification and Abundance Data in YeastMine
December 17, 2014
Have you ever wondered what’s happening to your favorite protein as it’s hanging out in the cell? SGD’s advanced search tool, YeastMine, now includes four new templates that can be used to find protein modification and abundance data.
The Gene -> Protein Modifications template retrieves phosphorylation, ubiquitination, succinylation, acetylation and methylation data, currently curated from the following 11 publications: Peng et al. 2003, Hitchcock et al. 2003, Seyfried et al. 2008, Vogtle et al. 2009, Ziv et al. 2011, Mommen et al. 2012, Henriksen et al. 2012, Swaney et al. 2013, Kolawa et al. 2013, Weinert et al. 2013, and Wang et al. 2014.
The Gene -> Experimental N-termini and N-terminal modifications template retrieves experimentally-determined amino-terminal sequence and acetylation data, currently curated from Vogtle et al. 2009 and Mommen et al. 2012.
Lastly, two new templates pull protein abundance data curated from Ghaemmaghami et al. 2003. Gene -> Protein Abundance retrieves molecules/cell counts for a gene or list of genes. The same data can be quickly filtered using the Retrieve -> Proteins in a given molecules/cell abundance range template.
Please explore these new YeastMine protein data templates, and send us your feedback.
Categories: Data updates, New Data
New Alternative Reference Genomes
December 08, 2014
At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are making progress in our move toward providing multiple reference genomes. To this end, the following new S. cerevisiae genomes have been incorporated into SGD as “Alternative References”: CEN.PK, D273-10B, FL100, JK9-3d, RM11-1a, SEY6210, SK1, Sigma1278b, W303, X2180-1A, Y55. These genomes are accessible via Sequence, Strain, and Contig pages, and are the genomes for which we have curated the most phenotype data, and for which we aim to curate specific functional information. It is important to emphasize that we are not abandoning a standard sequence; S288C is still in place as “The Reference Genome”. However, we do recognize that it is helpful for students and researchers to be able to ‘shift the reference’, selecting the genome that is most appropriate and informative for a specific area of study.
These new genome sequences have been also been added to SGD’s BLAST datasets, multiple sequence alignments, the Pattern Matching tool, and the Downloads site. Please explore these new genomes, and send us your feedback.
Categories: Data updates, New Data, Sequence
Tags: reference genome, Saccharomyces cerevisiae, strains
New Sequence, Chromosome, and Contig pages
August 25, 2014
New Sequence pages are now available in SGD for virtually every yeast gene (e.g., HMRA1 Sequence page), and include genomic sequence annotations for the Reference Strain S288C, as well as several Alternative Reference Genomes from strains such as CEN.PK, RM11-1a, Sigma1278b, and W303 (more Alternative References coming soon). Each page includes an Overview section containing descriptive information, maps depicting genomic context in Reference Strain S288C (as shown below) and Alternative Reference strains, as well as chromosomal and relative coordinates in S288C.
The sequence itself includes display options for genomic DNA, coding DNA, or translated protein.
Also available on each Sequence page are links to redesigned S288C Chromosome pages, links to new Contig pages for Alternative Reference Genomes, and a Downloads menu for easy access to DNA sequences of several other industrial strains and environmental isolates. The new Sequence, Chromosome, and Contig pages make use of many of the features you enjoy on other new or redesigned pages at SGD, including graphical display of data, sortable tables, and responsive visualizations. The Sequence pages also provide seamless access to other tools at SGD such as BLAST and Web Primer. Please explore these new pages, accessible via the Sequence tab on your favorite Locus Summary page, and send us your feedback.
Categories: Data updates, New Data, Sequence, Website changes