New & Noteworthy

SGD Newsletter, Fall 2021

December 14, 2021

About this newsletter:
This is the Fall 2021 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this newsletter as well as previous newsletters on our Community Wiki.

Contents

Protein Complex Page Updates

Complex3.png

SGD has made recent updates to our protein complex pages to improve clarity and ease of use. The new pages for each complex will have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a Gene Ontology page, and a Literature page. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.

If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.

Nomenclature Updates

SGD has long been the keeper of the official Saccharomyces cerevisiae gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38RPL1A, and OM45.

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

Legacy gene names

ORFOld gene nameNew gene name
YGL234WADE5,7ADE57
YER069WARG5,6ARG56
YBR208CDUR1,2DUR12
YIL154CIMP2′IMP21

New systematic nomenclature for yeast genes not in the reference genome

For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the last SGD newsletter will recall that, earlier this year, SGD adopted a new systematic nomenclature for the entire annotated complement of ncRNAs.

We have just put into place a new systematic nomenclature for S. cerevisiae genes that are not found in the reference genome of strain S288C (“non-reference” genes). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for “Yeast”, SC for “Saccharomyces cerevisiae”, and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like MAL21/YSC0004 and MATA/YSC0046, while others are more recent additions like XDH1/YSC0051. Going forward, as evidence is published pointing to other S. cerevisiae genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please let us know!

Would you like to see the shape of your protein?

Hog1 structure.png

SGD now contains links to AlphaFold in the Resources sections of the SummaryProtein, and Homology pages for every gene.

  • The links through SGD give quick access to EMBL’s European Bioinformatics Institute (EMBL-EBI), which offers a new, highly accurate tool for predicting protein structure with speed and clarity.
  • Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.
  • The predicted domains can then be compared to known protein structures (using a tool such as PDBeFold) to seek matches to characterized protein families.
  • Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

DIOPT Orthologs and New Queries in YeastMine

DIOPT-logo-integrative trans.png

We recently replaced HomoloGene, Ensembl, TreeFam and PANTHER homology datasets in YeastMine with homology data from DIOPT (DRSC integrative ortholog prediction tool). DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and PANTHER. Using the Gene->Non-fungal and S. cerevisiae Homologs pre-generated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further.

Pre-generated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations remain largely unchanged. You can begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the S. cerevisiae homologs of all human genes associated with disorders that contain the keyword “diabetes” (view search). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

Alliance of Genome Resources – Recent Release

alliance logo.png

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 4.1 this past August. Notable improvements and new features include:

  • Human and model organism high throughput (HTP) variant data
    • Human variants are imported from Ensembl
    • Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
    • Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
    • Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
    • Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
  • On Gene Pages, a new Pathways widget displays via tabs:
    • Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
    • Reactome reactions for gene products (e.g. human TP53 Gene page)
    • Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
  • Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
  • AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
  • The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

Upcoming Conferences and Courses

  • Fungal Genetics – the premier meeting for the international community of fungal geneticists
    • Asilomar Conference Grounds, Pacific Grove, California (and Online)
    • March 15 – 20, 2022
  • 36th International Specialised Symposium on Yeasts (ISSY36) – Yeast Sea to Sky – Yeast in the Genomics Era
    • University of British Columbia, Vancouver
    • July 12 – 16, 2022
  • CSHL Yeast Genetics & Genomics – modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
    • Cold Spring Harbor Laboratory, NY
    • July 26 – August 15, 2022
  • Yeast Genetics Meeting – the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
    • University of California, Los Angeles
    • August 17 – 21, 2022

Gene Ontology Consortium Fall 2021 Meeting

logo GOC.png

From October 12-14, SGD biocurators attended the Gene Ontology Consortium’s Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:

  • LitSuggest – web-based system for biomedical literature recommendation and curation
  • ECO, Evidence and Conclusions Ontology – terms used to describe types of evidence and assertion methods
  • PAINT, Phylogenetic Annotation and INference Tool from PANTHER – orthology between reference genome genes and human disease genes

Happy Holidays from SGD!

SnowShmoo.png

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.

Categories: Newsletter

Tags: Newsletter, Saccharomyces cerevisiae

Protein Complex Page Updates

December 01, 2021

SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.

Summary page and new Literature page

If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.

Categories: Announcements, Data updates, Website changes

Tags: protein complex, Saccharomyces cerevisiae

New links to AlphaFold 3D Predicted Protein Structure Database

November 09, 2021

  • The links through SGD give quick access to EMBLEuropean Bioinformatics Institute‘s new, highly accurate tool for predicting protein structure.
  • Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.
  • The predicted domains can then be compared to known protein structures (using a tool such as PDBeFold to seek matches to characterized protein families).
  • Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.
Structure of Hog1p

Categories: Data updates

Tags: AlphaFold, new tools

Updates to legacy gene names

November 05, 2021

SGD has long been the keeper of the official Saccharomyces cerevisiae gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years. 

The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38RPL1A, and OM45

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

ORFOld gene nameNew gene name
YGL234WADE5,7ADE57
YER069WARG5,6ARG56
YBR208CDUR1,2DUR12
YIL154CIMP2′IMP21

Categories: Announcements, Data updates

Tags: gene nomenclature

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:

R64.3 Annotation update details

ChrFeatureDescription of changeReference
IIYNCB0008W aka GAL10-ncRNANew ncRNA antisense to GAL10coordinates 276805..280645Houseley et al 2008 PMID:19061643,Pinskaya et al 2009 PMID:19407817,
Geisler et al 2012 PMID:22226051
IIYNCB0014W aka TBRT/XUT_2F-154New ncRNA antisense to TAT1coordinates 376610..378633Awasthi et al 2020 PMID:32081726
IIIRE/RE301New recombination enhancercoordinates 29108..29809Wu and Haber 1996 PMID:8861911
VYELWdelta27New Ty1 LTRcoordinates 449274..449626Nene et al 2018 PMID:29320491
VHPA3/YEL066WMoved translation start to Met19old coordinates: 26667..27206new coordinates: 26721..27206Sampath et al 2013 PMID:23775086
VIIOTO1/YGR227C-ANew ORFcoordinates 949052..949225 CrickMakanae et al 2015 PMID:25781884
VIIROK1/YGL171WTwo new uORFscoordinates uORF1: 182286..182407coordinates uORF2: 182291..182329Jeon and Kim 2010 PMID:20969870
VIIIYHR052C-BNew ORFcoordinates: 212519..212692 CrickHe et al 2018 PMID:29897761
VIIIYHR054C-BNew ORFcoordinates: 214517..214690 CrickHe et al 2018 PMID:29897761
VIIISUT169/YNCH0011WNew ncRNAcoordinates 378254..379237Xu et al 2009 PMID:19169243,Geisler et al 2012 PMID:22226051,
Huber et al 2016 PMID:27292640,
Bunina et al 2017 PMID:28977638
XYJR012CMoved start to Met76old coordinates: 459795..460418 Cricknew coordinates: 459795..460193 CrickSadhu et al 2018 PMID:29632376
XYJR107C-ANew ORFcoordinates 628457..628693 CrickYagoub et al 2015 PMID:26554900,
He et al 2018 PMID:29897761
XIYKL104W-ANew ORFcoordinates 245032..245286He et al 2018 PMID:29897761
XIIYLR379W-ANew ORFcoordinates: 877444..877716Internal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462
XIINTS1-2NTS2-1NTS2-2Change feature_type/SO_term from SO:0001637 rRNA_gene to SO:0000183 non_transcribed_region
XIIILDO45/YMR147WShift stop to be same as LDO16/YMR148W, add intronold coordinates 559199..559870new coordinates 559199..559780, 560156..560812Eisenberg-Bord et al 2018 PMID:29187527
XIIIYMR008C-ANew ORFcoordinates 283081..283548 CrickInternal reanalysis of results from Song et al 2015 to find and annotate missing S288C ORFs PMID:25781462
XIIIYNCM0001W aka PHO84 lncRNANew ncRNAcoordinates: 23564..26578Camblong et al 2007 PMID:18022365
XIVLTO1/YNL260CMove start to Met37old coordinates: 156859..157455 Cricknew coordinates: 156859..157347 CrickPaul et al 2015 PMID:26182403
XVIYNCP0002W aka GAL4 lncRNANew ncRNAcoordinates: 79562..82648Geisler et al 2012 PMID:22226051

New systematic nomenclature system for noncoding RNA genes

ChrSystematic_nameGene_nameAliasFeature_typeCoordinatesStrand
IYNCA0001WHRA1ncRNA gene99305..99868+
IYNCA0002WTRN1tP(UGG)A, tRNA-ProtRNA gene139152..139254+
IYNCA0003WSNR18snR18snoRNA gene142367..142468+
IYNCA0004WTGA1tA(UGC)A, tRNA-AlatRNA gene166267..166339+
IYNCA0005WSUP56tL(CAA)A, tRNA-LeutRNA gene181141..181254+
IYNCA0006CtS(AGA)A, tRNA-SertRNA gene182522..182603
IIYNCB0001WtL(UAA)B1, tRNA-LeutRNA gene9583..9666+
IIYNCB0002WtF(GAA)B, tRNA-PhetRNA gene36398..36488+
IIYNCB0003WSNR56snR56snoRNA gene88190..88277+
IIYNCB0004WtI(AAU)B, tRNA-IletRNA gene197494..197567+
IIYNCB0005CtG(GCC)B, tRNA-GlytRNA gene197629..197699
IIYNCB0006WtS(AGA)B, tRNA-SertRNA gene227075..227156+
IIYNCB0007WtT(AGU)B, tRNA-ThrtRNA gene266378..266450+
IIYNCB0008WGAL10-ncRNAncRNA gene276805..280645+
IIYNCB0009CSNR161snR161snoRNA gene307185..307345
IIYNCB0010WTLC1telomerase RNA gene307587..308887+
IIYNCB0011CtV(UAC)B, tRNA-ValtRNA gene326792..326865
IIYNCB0012WtL(UAA)B2, tRNA-LeutRNA gene347603..347686+
IIYNCB0013WtQ(UUG)B, tRNA-GlntRNA gene350827..350898+
IIYNCB0014WTBRTXUT_2F-154ncRNA gene376610..378633+
IIYNCB0015WtR(UCU)B, tRNA-ArgtRNA gene405878..405949+
IIYNCB0016WtD(GUC)B, tRNA-AsptRNA gene405960..406031+
IIYNCB0017CtC(GCA)B, tRNA-CystRNA gene643007..643078
IIYNCB0018WtE(UUC)B, tRNA-GlutRNA gene645167..645238+
IIYNCB0019CLSR1snRNA gene680688..681862
IIIYNCC0001CtE(UUC)C, tRNA-GlutRNA gene82462..82533
IIIYNCC0002WSUP53tL(CAA)C, tRNA-LeutRNA gene90859..90972+
IIIYNCC0003CSNR43snR43snoRNA gene107504..107712
IIIYNCC0004CSUF2tP(AGG)C, tRNA-ProtRNA gene123577..123648
IIIYNCC0005WtN(GUU)C, tRNA-AsntRNA gene127716..127789+
IIIYNCC0006CSNR33snR33snoRNA gene142364..142546
IIIYNCC0007CSUF16tG(GCC)C, tRNA-GlytRNA gene142701..142771
IIIYNCC0008WtM(CAU)C, tRNA-MettRNA gene149920..149991+
IIIYNCC0009CtK(CUU)C, tRNA-LystRNA gene151284..151356
IIIYNCC0010CtQ(UUG)C, tRNA-GlntRNA gene168301..168372
IIIYNCC0011WSNR65snR65snoRNA gene177183..177282+
IIIYNCC0012CSNR189snR189snoRNA gene178610..178798
IIIYNCC0013WSUP61tS(CGA)C, tRNA-SertRNA gene227942..228042+
IIIYNCC0014WtT(AGU)C, tRNA-ThrtRNA gene295484..295556+
IVYNCD0001WtG(GCC)D1, tRNA-GlytRNA gene83548..83618+
IVYNCD0002CSNR63snR63snoRNA gene323217..323471
IVYNCD0003WtK(UUU)D, tRNA-LystRNA gene359577..359672+
IVYNCD0004WtA(AGC)D, tRNA-AlatRNA gene410379..410451+
IVYNCD0005CtT(AGU)D, tRNA-ThrtRNA gene434264..434336
IVYNCD0006WtS(AGA)D1, tRNA-SertRNA gene437772..437853+
IVYNCD0007CtV(UAC)D, tRNA-ValtRNA gene488797..488870
IVYNCD0008WtL(UAA)D, tRNA-LeutRNA gene519743..519826+
IVYNCD0009WtQ(UUG)D1, tRNA-GlntRNA gene520972..521043+
IVYNCD0010CSNR47snR47snoRNA gene541602..541700
IVYNCD0011WtR(UCU)D, tRNA-ArgtRNA gene568882..568953+
IVYNCD0012WtD(GUC)D, tRNA-AsptRNA gene568964..569035+
IVYNCD0013CtR(ACG)D, tRNA-ArgtRNA gene619969..620041
IVYNCD0014CtQ(UUG)D2, tRNA-GlntRNA gene645153..645224
IVYNCD0015CtI(AAU)D, tRNA-IletRNA gene668007..668080
IVYNCD0016CtQ(UUG)D3, tRNA-GlntRNA gene802731..802802
IVYNCD0017WtI(UAU)D, tRNA-IletRNA gene884361..884493+
IVYNCD0018WSUP2tY(GUA)D, tRNA-TyrtRNA gene946312..946400+
IVYNCD0019CtS(AGA)D2, tRNA-SertRNA gene980974..981055
IVYNCD0020WtG(GCC)D2, tRNA-GlytRNA gene992832..992902+
IVYNCD0021CtE(CUC)D, tRNA-GlutRNA gene1017207..1017278
IVYNCD0022CtV(CAC)D, tRNA-ValtRNA gene1075472..1075544
IVYNCD0023CtF(GAA)D, tRNA-PhetRNA gene1095370..1095461
IVYNCD0024CtX(XXX)DtRNA gene1150842..1150941
IVYNCD0025WEMT1tM(CAU)D, tRNA-MettRNA gene1175829..1175901+
IVYNCD0026WtK(CUU)D1, tRNA-LystRNA gene1201750..1201822+
IVYNCD0027CSUF3tG(CCC)D, tRNA-GlytRNA gene1257008..1257079
IVYNCD0028WtS(AGA)D3, tRNA-SertRNA gene1305630..1305712+
IVYNCD0029CtK(CUU)D2, tRNA-LystRNA gene1352466..1352538
IVYNCD0030WSNR13snR13snoRNA gene1402919..1403042+
IVYNCD0031CtL(CAA)D, tRNA-LeutRNA gene1461715..1461829
IVYNCD0032CSNR84snR84snoRNA gene1492477..1493026
VYNCE0001CSNR80snR80snoRNA gene52150..52320
VYNCE0002WSNR67snR67snoRNA gene61352..61433+
VYNCE0003WSNR53snR53snoRNA gene61699..61789+
VYNCE0004CtG(GCC)E, tRNA-GlytRNA gene61890..61960
VYNCE0005WtS(AGA)E, tRNA-SertRNA gene86604..86685+
VYNCE0006WIMT4tM(CAU)E, tRNA-MettRNA gene100133..100204+
VYNCE0007CRPR1ncRNA gene117667..118035
VYNCE0008CtQ(UUG)E2, tRNA-GlntRNA gene131082..131153
VYNCE0009CtK(CUU)E1, tRNA-LystRNA gene135425..135497
VYNCE0010WtR(UCU)E, tRNA-ArgtRNA gene138666..138737+
VYNCE0011CSNR14snR14snRNA gene167427..167586
VYNCE0012WtE(UUC)E1, tRNA-GlutRNA gene177099..177170+
VYNCE0013WtH(GUG)E1, tRNA-HistRNA gene207357..207428+
VYNCE0014WtQ(UUG)E1, tRNA-GlntRNA gene250286..250357+
VYNCE0015CSUP19tS(UGA)E, tRNA-SertRNA gene288443..288524
VYNCE0016CtA(UGC)E, tRNA-AlatRNA gene312023..312095
VYNCE0017WSRG1ncRNA gene322212..322762+
VYNCE0018WtE(UUC)E2, tRNA-GlutRNA gene354934..355005+
VYNCE0019WSNR4snR4snoRNA gene424698..424883+
VYNCE0020CSNR52snR52snoRNA gene431129..431220
VYNCE0021CtH(GUG)E2, tRNA-HistRNA gene434541..434612
VYNCE0022CtK(CUU)E2, tRNA-LystRNA gene435752..435824
VYNCE0023WtV(AAC)E1, tRNA-ValtRNA gene438700..438773+
VYNCE0024WSCR1ncRNA gene441987..442508+
VYNCE0025CtI(AAU)E1, tRNA-IletRNA gene443202..443275
VYNCE0026WtV(AAC)E2, tRNA-ValtRNA gene469457..469530+
VYNCE0027CtE(UUC)E3, tRNA-GlutRNA gene487331..487402
VYNCE0028CtR(ACG)E, tRNA-ArgtRNA gene492352..492424
VYNCE0029CtI(AAU)E2, tRNA-IletRNA gene551285..551358
VIYNCF0001CRUF21ncRNA gene57815..58521
VIYNCF0002WSUF9tP(UGG)F, tRNA-ProtRNA gene101376..101478+
VIYNCF0003CRUF20ncRNA gene131061..131503
VIYNCF0004CtN(GUU)F, tRNA-AsntRNA gene137486..137559
VIYNCF0005CtF(GAA)F, tRNA-PhetRNA gene157916..158007
VIYNCF0006WSUF20tG(GCC)F1, tRNA-GlytRNA gene162228..162298+
VIYNCF0007WSUP11tY(GUA)F1, tRNA-TyrtRNA gene167437..167525+
VIYNCF0008CtG(GCC)F2, tRNA-GlytRNA gene180974..181044
VIYNCF0009CtS(GCU)F, tRNA-SertRNA gene191513..191613
VIYNCF0010CRUF22ncRNA gene199299..199813
VIYNCF0011CtA(AGC)F, tRNA-AlatRNA gene204924..204996
VIYNCF0012CSUP6tY(GUA)F2, tRNA-TyrtRNA gene210619..210707
VIYNCF0013WRUF23ncRNA gene221714..221967+
VIYNCF0014CtK(CUU)F, tRNA-LystRNA gene226688..226760
VIIYNCG0001CRME3ncRNA gene33109..35013
VIIYNCG0002CtV(AAC)G3, tRNA-ValtRNA gene73829..73902
VIIYNCG0003CtH(GUG)G1, tRNA-HistRNA gene110625..110696
VIIYNCG0004WtK(UUU)G1, tRNA-LystRNA gene115488..115583+
VIIYNCG0005WtK(CUU)G1, tRNA-LystRNA gene122269..122341+
VIIYNCG0006CRME2ncRNA gene141898..144120
VIIYNCG0007CtK(CUU)G2, tRNA-LystRNA gene185714..185786
VIIYNCG0008WtL(CAA)G1, tRNA-LeutRNA gene205521..205634+
VIIYNCG0009CtW(CCA)G1, tRNA-TrptRNA gene287350..287455
VIIYNCG0010WSNR82snR82snoRNA gene316788..317055+
VIIYNCG0011WtH(GUG)G2, tRNA-HistRNA gene319781..319852+
VIIYNCG0012WSOE1tE(UUC)G1, tRNA-GlutRNA gene328583..328654+
VIIYNCG0013WSNR10snR10snoRNA gene345986..346230+
VIIYNCG0014CSNR39snR39snoRNA gene365163..365251
VIIYNCG0015CSNR39BsnR39BsnoRNA gene366374..366469
VIIYNCG0016CtE(UUC)G2, tRNA-GlutRNA gene401527..401598
VIIYNCG0017WtR(UCU)G1, tRNA-ArgtRNA gene405470..405541+
VIIYNCG0018CtV(AAC)G1, tRNA-ValtRNA gene412294..412367
VIIYNCG0019WSUP54tL(CAA)G2, tRNA-LeutRNA gene423092..423205+
VIIYNCG0020CtF(GAA)G, tRNA-PhetRNA gene440716..440807
VIIYNCG0021WtD(GUC)G1, tRNA-AsptRNA gene531610..531681+
VIIYNCG0022WtE(UUC)G3, tRNA-GlutRNA gene541850..541921+
VIIYNCG0023CtD(GUC)G2, tRNA-AsptRNA gene544577..544648
VIIYNCG0024WSNR46snR46snoRNA gene545370..545566+
VIIYNCG0025CtS(AGA)G, tRNA-SertRNA gene561662..561743
VIIYNCG0026WSNR48snR48snoRNA gene609584..609696+
VIIYNCG0027WtT(UGU)G1, tRNA-ThrtRNA gene661749..661820+
VIIYNCG0028WtL(GAG)G, tRNA-LeutRNA gene700675..700756+
VIIYNCG0029CtK(UUU)G2, tRNA-LystRNA gene700953..701048
VIIYNCG0030CtC(GCA)G, tRNA-CystRNA gene707108..707179
VIIYNCG0031WtN(GUU)G, tRNA-AsntRNA gene731137..731210+
VIIYNCG0032WtR(UCU)G3, tRNA-ArgtRNA gene736340..736411+
VIIYNCG0033WtI(AAU)G, tRNA-IletRNA gene739122..739195+
VIIYNCG0034WtA(AGC)G, tRNA-AlatRNA gene774349..774421+
VIIYNCG0035WSUF4tG(UCC)G, tRNA-GlytRNA gene779616..779687+
VIIYNCG0036WtA(UGC)G, tRNA-AlatRNA gene794417..794489+
VIIYNCG0037WtV(AAC)G2, tRNA-ValtRNA gene823482..823555+
VIIYNCG0038CtR(UCU)G2, tRNA-ArgtRNA gene828723..828794
VIIYNCG0039WtG(GCC)G1, tRNA-GlytRNA gene845649..845719+
VIIYNCG0040CtL(CAA)G3, tRNA-LeutRNA gene857378..857491
VIIYNCG0041WtK(CUU)G3, tRNA-LystRNA gene876394..876466+
VIIYNCG0042CtW(CCA)G2, tRNA-TrptRNA gene878710..878815
VIIYNCG0043CtG(GCC)G2, tRNA-GlytRNA gene930953..931023
VIIYNCG0044CSNR7-LsnR7-LsnRNA gene939459..939672
VIIYNCG0045CSNR7-SsnR7-SsnRNA gene939494..939672
VIIYNCG0046WtT(UGU)G2, tRNA-ThrtRNA gene1004216..1004287+
VIIIYNCH0001WtH(GUG)H, tRNA-HistRNA gene62755..62826+
VIIIYNCH0002CtV(AAC)H, tRNA-ValtRNA gene85298..85371
VIIIYNCH0003CtT(AGU)H, tRNA-ThrtRNA gene116107..116179
VIIIYNCH0004CtS(AGA)H, tRNA-SertRNA gene133026..133107
VIIIYNCH0005WtQ(UUG)H, tRNA-GlntRNA gene134321..134392+
VIIIYNCH0006CtA(AGC)H, tRNA-AlatRNA gene146242..146314
VIIIYNCH0007WRUF5-1ncRNA gene212409..213118+
VIIIYNCH0008WRUF5-2ncRNA gene214407..215116+
VIIIYNCH0009CtF(GAA)H1, tRNA-PhetRNA gene237848..237939
VIIIYNCH0010CtF(GAA)H2, tRNA-PhetRNA gene358478..358569
VIIIYNCH0011WSUT169ncRNA gene378254..379237+
VIIIYNCH0012WSNR32snR32snoRNA gene381540..381727+
VIIIYNCH0013CSUF8tP(UGG)H, tRNA-ProtRNA gene388893..388995
VIIIYNCH0014WSNR71snR71snoRNA gene411228..411317+
VIIIYNCH0015WtT(UGU)H, tRNA-ThrtRNA gene466990..467061+
VIIIYNCH0016CtV(CAC)H, tRNA-ValtRNA gene475706..475778
IXYNCI0001WSNR68snR68snoRNA gene97111..97246+
IXYNCI0002WtT(AGU)I1, tRNA-ThrtRNA gene175031..175103+
IXYNCI0003CtI(AAU)I1, tRNA-IletRNA gene183440..183513
IXYNCI0004WtE(CUC)I, tRNA-GlutRNA gene197592..197663+
IXYNCI0005WtI(AAU)I2, tRNA-IletRNA gene210665..210738+
IXYNCI0006WSUP17tS(UGA)I, tRNA-SertRNA gene248850..248931+
IXYNCI0007CtK(CUU)I, tRNA-LystRNA gene300228..300300
IXYNCI0008CtD(GUC)I1, tRNA-AsptRNA gene324303..324374
IXYNCI0009WtT(AGU)I2, tRNA-ThrtRNA gene325748..325820+
IXYNCI0010CtD(GUC)I2, tRNA-AsptRNA gene336349..336420
IXYNCI0011WtE(UUC)I, tRNA-GlutRNA gene370417..370488+
IXYNCI0012ICR1ncRNA gene393884..397082
IXYNCI0013WPWR1ncRNA gene395999..396939+
XYNCJ0001CtT(AGU)J, tRNA-ThrtRNA gene59100..59172
XYNCJ0002CtE(UUC)J, tRNA-GlutRNA gene115939..116010
XYNCJ0003CSNR128snR128snoRNA gene139566..139691
XYNCJ0004CSNR190snR190snoRNA gene139761..139950
XYNCJ0005CtA(AGC)J, tRNA-AlatRNA gene197313..197385
XYNCJ0006WtD(GUC)J1, tRNA-AsptRNA gene204735..204806+
XYNCJ0007CSNR37snR37snoRNA gene228094..228479
XYNCJ0008WtR(ACG)J, tRNA-ArgtRNA gene233939..234011+
XYNCJ0009CSNR60snR60snoRNA gene349130..349233
XYNCJ0010WSUP7tY(GUA)J1, tRNA-TyrtRNA gene354244..354332+
XYNCJ0011WtR(UCU)J1, tRNA-ArgtRNA gene355374..355445+
XYNCJ0012WtD(GUC)J2, tRNA-AsptRNA gene355456..355527+
XYNCJ0013CtD(GUC)J3, tRNA-AsptRNA gene374424..374495
XYNCJ0014CtR(UCU)J2, tRNA-ArgtRNA gene374506..374577
XYNCJ0015WtV(AAC)J, tRNA-ValtRNA gene378360..378433+
XYNCJ0016CEMT5tM(CAU)J1, tRNA-MettRNA gene391043..391115
XYNCJ0017CtG(GCC)J1, tRNA-GlytRNA gene396726..396796
XYNCJ0018WtK(CUU)J, tRNA-LystRNA gene414966..415038+
XYNCJ0019CtW(CCA)J, tRNA-TrptRNA gene415931..416036
XYNCJ0020WEMT3tM(CAU)J2, tRNA-MettRNA gene422937..423009+
XYNCJ0021CSUP51tL(UAA)J, tRNA-LeutRNA gene424432..424515
XYNCJ0022CIMT3tM(CAU)J3, tRNA-MettRNA gene517813..517884
XYNCJ0023CtS(AGA)J, tRNA-SertRNA gene524012..524093
XYNCJ0024WSUF23tG(GCC)J2, tRNA-GlytRNA gene531828..531898+
XYNCJ0025WHSX1tR(CCU)J, tRNA-ArgtRNA gene538555..538626+
XYNCJ0026WtD(GUC)J4, tRNA-AsptRNA gene541508..541579+
XYNCJ0027CSUP4tY(GUA)J2, tRNA-TyrtRNA gene542956..543044
XYNCJ0028CIRT1ncRNA gene605936..607424
XYNCJ0029WtL(UAG)J, tRNA-LeutRNA gene617919..618019+
XYNCJ0030WSNR3snR3snoRNA gene663749..663942+
XIYNCK0001WSNR64snR64snoRNA gene38811..38911+
XIYNCK0002CTRT2tT(CGU)K, tRNA-ThrtRNA gene46735..46806
XIYNCK0003WtN(GUU)K, tRNA-AsntRNA gene74624..74697+
XIYNCK0004WtL(UAA)K, tRNA-LeutRNA gene84208..84291+
XIYNCK0005CtE(UUC)K, tRNA-GlutRNA gene141018..141089
XIYNCK0006CtR(UCU)K, tRNA-ArgtRNA gene162487..162558
XIYNCK0007WtK(CUU)K, tRNA-LystRNA gene202999..203071+
XIYNCK0008WtA(AGC)K1, tRNA-AlatRNA gene219895..219967+
XIYNCK0009WSNR38snR38snoRNA gene283185..283279+
XIYNCK0010WtW(CCA)K, tRNA-TrptRNA gene302918..303023+
XIYNCK0011CtV(AAC)K1, tRNA-ValtRNA gene308144..308217
XIYNCK0012CtH(GUG)K, tRNA-HistRNA gene313401..313472
XIYNCK0013WSNR69snR69snoRNA gene364776..364876+
XIYNCK0014WtV(AAC)K2, tRNA-ValtRNA gene379680..379753+
XIYNCK0015CSNR87snR87snoRNA gene431030..431138
XIYNCK0016WtL(CAA)K, tRNA-LeutRNA gene458557..458670+
XIYNCK0017WtR(ACG)K, tRNA-ArgtRNA gene490968..491040+
XIYNCK0018CtD(GUC)K, tRNA-AsptRNA gene513332..513403
XIYNCK0019WtA(AGC)K2, tRNA-AlatRNA gene517988..518060+
XIYNCK0020CSNR42snR42snoRNA gene559016..559366
XIYNCK0021WtK(UUU)K, tRNA-LystRNA gene578965..579060+
XIIYNCL0001WtP(UGG)L, tRNA-ProtRNA gene92548..92650+
XIIYNCL0002CtS(AGA)L, tRNA-SertRNA gene167944..168025
XIIYNCL0003WSNR30snR30snoRNA gene198784..199389+
XIIYNCL0004CtA(UGC)L, tRNA-AlatRNA gene214883..214955
XIIYNCL0005CSNR79snR79snoRNA gene348427..348510
XIIYNCL0006WSNR6snR6snRNA gene366235..366346+
XIIYNCL0007WtR(ACG)L, tRNA-ArgtRNA gene374355..374427+
XIIYNCL0008WtD(GUC)L1, tRNA-AsptRNA gene427132..427203+
XIIYNCL0009CtQ(UUG)L, tRNA-GlntRNA gene448650..448721
XIIYNCL0010CRDN37-1rRNA gene451575..458432
XIIYNCL0011CETS2-1rRNA gene451575..451785
XIIYNCL0012CRDN25-1rRNA gene451786..455181
XIIYNCL0013CITS2-1rRNA gene455182..455413
XIIYNCL0014CRDN58-1rRNA gene455414..455571
XIIYNCL0015CITS1-1rRNA gene455572..455932
XIIYNCL0016CRDN18-1rRNA gene455933..457732
XIIYNCL0017CETS1-1rRNA gene457733..458432
XIIYNCL0018WRDN5-1rRNA gene459676..459796+
XIIYNCL0019CETS2-2rRNA gene460712..460922
XIIYNCL0020CRDN37-2rRNA gene460712..467569
XIIYNCL0021CRDN25-2rRNA gene460923..464318
XIIYNCL0022CITS2-2rRNA gene464319..464550
XIIYNCL0023CRDN58-2rRNA gene464551..464708
XIIYNCL0024CITS1-2rRNA gene464709..465069
XIIYNCL0025CRDN18-2rRNA gene465070..466869
XIIYNCL0026CETS1-2rRNA gene466870..467569
XIIYNCL0027WRDN5-2rRNA gene468813..468931+
XIIYNCL0028WRDN5-3rRNA gene472465..472583+
XIIYNCL0029WRDN5-4rRNA gene482045..482163+
XIIYNCL0030WRDN5-5rRNA gene485697..485815+
XIIYNCL0031WRDN5-6rRNA gene489349..489469+
XIIYNCL0032CtL(UAG)L1, tRNA-LeutRNA gene592519..592619
XIIYNCL0033CtI(UAU)L, tRNA-IletRNA gene605300..605432
XIIYNCL0034WtL(CAA)L, tRNA-LeutRNA gene628383..628497+
XIIYNCL0035CtA(AGC)L, tRNA-AlatRNA gene656934..657006
XIIYNCL0036CtV(AAC)L, tRNA-ValtRNA gene687859..687932
XIIYNCL0037WtL(UAG)L2, tRNA-LeutRNA gene732090..732190+
XIIYNCL0038WtI(AAU)L1, tRNA-IletRNA gene734802..734875+
XIIYNCL0039WtX(XXX)LtRNA gene784354..784453+
XIIYNCL0040WtD(GUC)L2, tRNA-AsptRNA gene793918..793989+
XIIYNCL0041CSNR61snR61snoRNA gene794486..794575
XIIYNCL0042CSNR55snR55snoRNA gene794697..794794
XIIYNCL0043CSNR57snR57snoRNA gene794937..795024
XIIYNCL0044WtE(UUC)L, tRNA-GlutRNA gene797178..797249+
XIIYNCL0045WTRR4tR(CCG)L, tRNA-ArgtRNA gene818609..818680+
XIIYNCL0046WSNR44snR44snoRNA gene856710..856920+
XIIYNCL0047WtK(UUU)L, tRNA-LystRNA gene875376..875471+
XIIYNCL0048WSNR34snR34snoRNA gene899180..899382+
XIIYNCL0049CtL(UAA)L, tRNA-LeutRNA gene962972..963055
XIIYNCL0050CtN(GUU)L, tRNA-AsntRNA gene975983..976056
XIIYNCL0051CtI(AAU)L2, tRNA-IletRNA gene1052071..1052144
XIIIYNCM0001WPHO84 lncRNAncRNA gene23564..26578+
XIIIYNCM0002CSNR85snR85snoRNA gene67768..67938
XIIIYNCM0003WZOD1ncRNA gene91970..92027+
XIIIYNCM0004CtR(UCU)M2, tRNA-ArgtRNA gene131825..131896
XIIIYNCM0005CSNR54snR54snoRNA gene163535..163620
XIIIYNCM0006WSUP5tY(GUA)M1, tRNA-TyrtRNA gene168795..168883+
XIIIYNCM0007CtG(GCC)M, tRNA-GlytRNA gene183898..183968
XIIIYNCM0008CSUF7tP(UGG)M, tRNA-ProtRNA gene196068..196170
XIIIYNCM0009CtS(AGA)M, tRNA-SertRNA gene259158..259239
XIIIYNCM0010WtE(UUC)M, tRNA-GlutRNA gene290801..290872+
XIIIYNCM0011WSNR78snR78snoRNA gene297278..297364+
XIIIYNCM0012WSNR77snR77snoRNA gene297506..297593+
XIIIYNCM0013WSNR76snR76snoRNA gene297725..297833+
XIIIYNCM0014WSNR75snR75snoRNA gene297918..298006+
XIIIYNCM0015WSNR74snR74snoRNA gene298138..298225+
XIIIYNCM0016WSNR73snR73snoRNA gene298307..298412+
XIIIYNCM0017WSNR72snR72snoRNA gene298554..298651+
XIIIYNCM0018CtA(AGC)M1, tRNA-AlatRNA gene321147..321219
XIIIYNCM0019WtF(GAA)M, tRNA-PhetRNA gene352280..352370+
XIIIYNCM0020WtH(GUG)M, tRNA-HistRNA gene363064..363135+
XIIIYNCM0021CtV(AAC)M1, tRNA-ValtRNA gene372445..372518
XIIIYNCM0022CtW(CCA)M, tRNA-TrptRNA gene379303..379408
XIIIYNCM0023CtV(AAC)M2, tRNA-ValtRNA gene420588..420661
XIIIYNCM0024WtD(GUC)M, tRNA-AsptRNA gene463554..463625+
XIIIYNCM0025CtK(CUU)M, tRNA-LystRNA gene480621..480693
XIIIYNCM0026CSNR24snR24snoRNA gene499984..500072
XIIIYNCM0027WtL(CAA)M, tRNA-LeutRNA gene504895..505008+
XIIIYNCM0028CEMT4tM(CAU)M, tRNA-MettRNA gene572883..572955
XIIIYNCM0029CtV(AAC)M3, tRNA-ValtRNA gene586636..586709
XIIIYNCM0030WSNR83snR83snoRNA gene626349..626654+
XIIIYNCM0031WSNR11snR11snoRNA gene652275..652532+
XIIIYNCM0032CRNA170ncRNA gene667288..667456
XIIIYNCM0033CtR(UCU)M1, tRNA-ArgtRNA gene747892..747963
XIIIYNCM0034CSNR86snR86snoRNA gene762110..763113
XIIIYNCM0035CtA(AGC)M2, tRNA-AlatRNA gene768369..768441
XIIIYNCM0036CCDC65tQ(CUG)M, tRNA-GlntRNA gene808246..808317
XIIIYNCM0037WSUP8tY(GUA)M2, tRNA-TyrtRNA gene837928..838016+
XIVYNCN0001WSNR40snR40snoRNA gene89210..89306+
XIVYNCN0002CSUF6tG(UCC)N, tRNA-GlytRNA gene96241..96312
XIVYNCN0003WtN(GUU)N1, tRNA-AsntRNA gene102716..102789+
XIVYNCN0004WtT(AGU)N1, tRNA-ThrtRNA gene104805..104877+
XIVYNCN0005CSNR19snR19snRNA gene230105..230672
XIVYNCN0006WtF(GAA)N, tRNA-PhetRNA gene374869..374959+
XIVYNCN0007WtL(CAA)N, tRNA-LeutRNA gene443006..443119+
XIVYNCN0008CtD(GUC)N, tRNA-AsptRNA gene519099..519169
XIVYNCN0009WtP(UGG)N1, tRNA-ProtRNA gene547094..547196+
XIVYNCN0010CtT(AGU)N2, tRNA-ThrtRNA gene560693..560765
XIVYNCN0011WtP(UGG)N2, tRNA-ProtRNA gene568115..568217+
XIVYNCN0012CtI(AAU)N1, tRNA-IletRNA gene569867..569940
XIVYNCN0013WNME1snoRNA gene585587..585926+
XIVYNCN0014WSNR66snR66snoRNA gene586090..586175+
XIVYNCN0015WtI(AAU)N2, tRNA-IletRNA gene602312..602385+
XIVYNCN0016CSUF10tP(AGG)N, tRNA-ProtRNA gene631846..631917
XIVYNCN0017WtN(GUU)N2, tRNA-AsntRNA gene632599..632672+
XIVYNCN0018WSNR49snR49snoRNA gene716120..716284+
XIVYNCN0019CSNR191snR191snoRNA gene721938..722211
XIVYNCN0020CtL(UAA)N, tRNA-LeutRNA gene726134..726217
XVYNCO0001CSUF1tG(UCC)O, tRNA-GlytRNA gene110962..111033
XVYNCO0002WtT(AGU)O1, tRNA-ThrtRNA gene113802..113874+
XVYNCO0003CSNR58snR58snoRNA gene136088..136183
XVYNCO0004CtG(GCC)O1, tRNA-GlytRNA gene226611..226681
XVYNCO0005WtN(GUU)O1, tRNA-AsntRNA gene228331..228404+
XVYNCO0006WSNR81snR81snoRNA gene234346..234546+
XVYNCO0007WSNR50snR50snoRNA gene259489..259578+
XVYNCO0008WtS(GCU)O, tRNA-SertRNA gene274673..274773+
XVYNCO0009WSUF17tG(GCC)O2, tRNA-GlytRNA gene282164..282234+
XVYNCO0010WSUP3tY(GUA)O, tRNA-TyrtRNA gene288192..288280+
XVYNCO0011WtP(UGG)O1, tRNA-ProtRNA gene301097..301198+
XVYNCO0012CtR(ACG)O, tRNA-ARgtRNA gene340299..340371
XVYNCO0013CtT(AGU)O2, tRNA-ThrtRNA gene354041..354113
XVYNCO0014CSNR9snR9snoRNA gene407948..408134
XVYNCO0015CSNR62snR62snoRNA gene409765..409864
XVYNCO0016WtK(UUU)O, tRNA-LystRNA gene438643..438738+
XVYNCO0017WSUF11tP(UGG)O2, tRNA-ProtRNA gene464450..464551+
XVYNCO0018WtN(GUU)O2, tRNA-AsntRNA gene487439..487512+
XVYNCO0019WtD(GUC)O, tRNA-AsptRNA gene571958..572029+
XVYNCO0020CSUF5tG(CCC)OtRNA gene594354..594425
XVYNCO0021CtV(AAC)OtRNA gene663812..663885
XVYNCO0022CSNR36snR36snoRNA gene680685..680866
XVYNCO0023WIMT1tM(CAU)O1, tRNA-MettRNA gene710201..710272+
XVYNCO0024CSNR35snR35snoRNA gene759326..759529
XVYNCO0025WSNR17AsnR17asnoRNA gene780107..780596+
XVYNCO0026WSNR8snR8snoRNA gene832332..832521+
XVYNCO0027CSNR31snR31snoRNA gene841958..842182
XVYNCO0028WSNR5snR5snoRNA gene842403..842606+
XVYNCO0029CtA(UGC)O, tRNA-AlatRNA gene854187..854259
XVYNCO0030WEMT2tM(CAU)O2, tRNA-MettRNA gene976421..976493+
XVYNCO0031WtP(UGG)O3, tRNA-ProtRNA gene980683..980787+
XVIYNCP0001CtW(CCA)P, tRNA-TrptRNA gene56169..56274
XVIYNCP0002WGAL4 lncRNAncRNA gene79562..82648+
XVIYNCP0003WSNR59snR59snoRNA gene173827..173904+
XVIYNCP0004CtE(UUC)P, tRNA-GlutRNA gene210192..210263
XVIYNCP0005CSNR17BsnR17bsnoRNA gene281056..281517
XVIYNCP0006CIMT2tM(CAU)P, tRNA-MettRNA gene338848..338919
XVIYNCP0007CtC(GCA)P1, tRNA-CystRNA gene435893..435964
XVIYNCP0008CtF(GAA)P1, tRNA-PhetRNA gene560198..560289
XVIYNCP0009WtG(GCC)P1, tRNA-GlytRNA gene572269..572339+
XVIYNCP0010WtK(CUU)P, tRNA-LystRNA gene582062..582134+
XVIYNCP0011CtF(GAA)P2, tRNA-PhetRNA gene622540..622631
XVIYNCP0012WSUP16tS(UGA)P, tRNA-SertRNA gene689565..689646+
XVIYNCP0013CSNR51snR51snoRNA gene718700..718806
XVIYNCP0014CSNR70snR70snoRNA gene718887..719050
XVIYNCP0015CSNR41snR41snoRNA gene719148..719242
XVIYNCP0016WtT(UGU)P, tRNA-ThrtRNA gene744284..744355+
XVIYNCP0017CtK(UUU)P, tRNA-LystRNA gene769207..769302
XVIYNCP0018CtC(GCA)P2, tRNA-CystRNA gene775765..775836
XVIYNCP0019WtN(GUU)P, tRNA-AsntRNA gene810676..810749+
XVIYNCP0020WtI(AAU)P1, tRNA-IletRNA gene819529..819602+
XVIYNCP0021WSNR45snR45snoRNA gene821732..821903+
XVIYNCP0022WtA(AGC)P, tRNA-AlatRNA gene856902..856974+
XVIYNCP0023WtG(GCC)P2, tRNA-GlytRNA gene860379..860449+
XVIYNCP0024CtI(AAU)P2, tRNA-IletRNA gene880296..880369
MitoYNCQ0001WtP(UGG)Q, tRNA-ProtRNA gene731..802+
MitoYNCQ0002W15S_RRNAQ0020rRNA gene6546..8194+
MitoYNCQ0003WtW(UCA)Q, tRNA-TrptRNA gene9374..9447+
MitoYNCQ0004WtE(UUC)Q, tRNA-GlutRNA gene35373..35444+
MitoYNCQ0005WtS(UGA)Q2, tRNA-SertRNA gene48201..48290+
MitoYNCQ0006W21S_RRNAQ0158rRNA gene58009..62447+
MitoYNCQ0007WtT(UGU)Q1, tRNA-ThrtRNA gene63862..63937+
MitoYNCQ0008WtC(GCA)Q, tRNA-CystRNA gene64415..64490+
MitoYNCQ0009WtH(GUG)Q, tRNA-HistRNA gene64596..64670+
MitoYNCQ0010WtL(UAA)Q, tRNA-LeutRNA gene66095..66179+
MitoYNCQ0011WtQ(UUG)Q, tRNA-GlntRNA gene66210..66285+
MitoYNCQ0012WtK(UUU)Q, tRNA-LystRNA gene67061..67134+
MitoYNCQ0013WtR(UCU)Q1, tRNA-ArgtRNA gene67309..67381+
MitoYNCQ0014WtG(UCC)Q, tRNA-GlytRNA gene67468..67542+
MitoYNCQ0015WtD(GUC)Q, tRNA-AsptRNA gene68322..68396+
MitoYNCQ0016WtS(GCU)Q1, tRNA-SertRNA gene69203..69288+
MitoYNCQ0017WtR(ACG)Q2, tRNA-ArgtRNA gene69289..69362+
MitoYNCQ0018WtA(UGC)Q, tRNA-AlatRNA gene69846..69921+
MitoYNCQ0019WtI(GAU)Q, tRNA-IletRNA gene70162..70237+
MitoYNCQ0020WtY(GUA)Q, tRNA-TyrtRNA gene70824..70907+
MitoYNCQ0021WtN(GUU)Q, tRNA-AsntRNA gene71433..71503+
MitoYNCQ0022WtM(CAU)Q1, tRNA-MettRNA gene72630..72705+
MitoYNCQ0023WtF(GAA)Q, tRNA-PhetRNA gene77431..77505+
MitoYNCQ0024CtT(UAG)Q2, tRNA-ThrtRNA gene78089..78162
MitoYNCQ0025WtV(UAC)Q, tRNA-ValtRNA gene78533..78608+
MitoYNCQ0026WtM(CAU)Q2, tRNA-MettRNA gene85035..85112+
MitoYNCQ0027WRPM1Q0285ncRNA gene85295..85777+

Various sequence and annotation files are available on SGD’s Downloads site.

Categories: Data updates

SGD Newsletter, Spring 2021

May 27, 2021

About this newsletter: 

This is the Spring 2021 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this newsletter as well as previous newsletters on our Community Wiki.

Contents

  1. R64.3 Annotation Update
  2. New Homology Pages
  3. Functional Complementation Data Available on References Pages
  4. YeastMine Updates and New Templates
  5. Textpresso Central Update
  6. Number of Curated Alleles Continues to Grow
  7. Alliance of Genome Resources – Disease Associations for model organisms
  8. Fungal Pathogen Genomics Workshop

R64.3 Annotation Update

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C.

The R64.3 annotation release, dated 2021-04-21, included various updates and additions:

Various sequence and annotation files are available on SGD’s Downloads site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the Details of 2021 Reference Genome Annotation Update R64.3 SGD Wiki page. 

New Homology Pages

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.
Image: 650 pixels
Image: 650 pixels

Functional Complementation Data Available on References Pages

Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

functional comp3.png

YeastMine Updates and New Templates

SGD has updated the current Gene–>UTRs YeastMine template with newly calculated 5′ and 3′ UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the Pelachano et al., 2013 study can be accessed in YeastMine using the new Gene–>Transcripts template. Both templates can be found under the “Templates” section of YeastMine under the “Expression” category.

Transcript and UTR YeastMine Templates

Textpresso Central Update

Textpresso has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:

  • Search results shown in the context of the full text
  • Custom corpus creation
  • Customizable annotation interface
  • Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on “Full-text Search” under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their About Us help section or (from Müller et al., 2018).

Number of Curated Alleles Continues to Grow

SGD now has approximately 13,000 alleles that are either fully or partially curated. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. SGD Curators continue to add new alleles or update existing ones as new information becomes available.

You can generate a list of all alleles in our database or find alleles for a specific gene using the Genes –> Alleles template in YeastMine

allele page.png

Alliance of Genome Resources – Disease Associations for model organisms

Did you know that you can find human disease associations for yeast genes and their orthologs in other key model organisms at the Alliance of Genome Resources?

SGD is a founding member of the Alliance of Genome Resources, which was established to facilitate the use of diverse model organisms in understanding the genetic and genomic bases of human biology, health, and disease.  Gene pages for yeast and other model organisms at the Alliance include a section for Disease Associations, including those for orthologous genes. Human diseases are represented using the Disease Ontology (DO).

allianceDiseaseTAZ1.png

Fungal Pathogen Genomics Workshop

From May 10th – 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the Virtual Fungal Pathogen Genomics Workshop hosted by Wellcome Connecting Science. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from FungiDBEnsemblFungiCGDMycoCosm, and JGI

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

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Categories: Newsletter

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

BREWMOR Workshop: Preparing Undergraduate Students for Research Experiences

February 03, 2021

BREWMOR: Bridging Research and Education With Model ORganisms (formerly BREW) will be hosting a virtual workshop titled, “Preparing Undergraduate Students for Research Experiences,” on Friday February 19th, 2021 from 4 – 6:30 PM US Eastern time.

After a very successful virtual BREW (Bridging Research and Education Workshop) in July of 2020 as part of the TAGC meeting, a steering committee was formed to coordinate activities of the BREW community. The name of the community was changed to BREWMOR: Bridging Research and Education With Model ORganisms, to include model organisms beyond yeast. 

A micro-BREWMOR event that will be held virtually on Friday February 19th, 2021 from 4-6:30 PM US Eastern time. The main purpose of the event is to provide a forum for social interactions and building a community for support and resource sharing.  The theme of this micro-BREWMOR will be “Preparing Undergraduate Students for Research Experiences”. The workshop will include a session related to the event’s main theme and opportunities to connect and collaborate with other undergraduate research mentors and teachers in multiple small breakout rooms focused on various topics.

Please register by February 8th at https://forms.gle/fdBCFxYjWuY38tSG6 . Registration is free. 

We hope you can join us at the micro-BREWMOR!

https://brewmor.weebly.com/gatherings.html

Categories: Announcements

Apply Now for the 2021 Fungal Pathogen Genomics (Virtual) Course

January 21, 2021

Fungal Pathogen Genomics is an exciting several day long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD, CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.

Please note: Due to the ongoing Covid-19 pandemic, the 2021 Fungal Pathogen Genomics course will be delivered in a virtual format.

Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers covering the following topics:

  • Comparative genomics, gene trees, whole-genome alignment
  • Identification of orthologs and orthology-based inference
  • Genome browsers and gene pages
  • RNA-Seq analysis and visualization in VEuPathDB Galaxy
  • Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
  • Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
  • Genetic interactions, virulence genes, secondary metabolites
  • Overview of ontology structure, evidence, available tools, slimming and enrichment
  • Introduction to annotation and curation of fungal genomes (e.g. Apollo in EnsemblFungi, FungiDB, and MycoCosm/JGI)

The application deadline for the Fungal Pathogen Genomics workshop to be held May 10-14, 2021 in virtual format is February 18, 2021.

Don’t miss out – apply now!

Categories: Announcements

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