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Configure Tracks on GWIPS-viz Genome Browser: S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3)
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-   Small Ribosomal Subunits (Footprints)    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Global Scanning Ribo-seq unique mappers from all studies
Archer 2016 Dynamics of ribosome scanning and recycling revealed by translation complex profiling. (Archer et al. 2016)
-   Elongating Ribosomes (A-site)    
Global Aggregate Ribosome profiles from all studies
Albert 2014 Genetic influences on translation in yeast. (Albert et al. 2014)
Archer 2016 Dynamics of ribosome scanning and recycling revealed by translation complex profiling.(Archer et al. 2016)
Baudin-Baillieu 2014 Ribosome profiles of elongating ribosomes from Sacchromyces cerevisiae [PSI+] and [psi-] strains (Baudin-Baillieu et al. 2014)
Beaupere17 CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes. (Beaupere et al. 2017)
Brar 2012 Ribosome profiles of elongating ribosomes from the yeast Saccharomyces cerevisiae during meiosis from traditional timecourse, strain ndt80, strain A14201, strain gb15 and strain mata/a (Brar et al. 2012)
Cai 2013 Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. (Cai et al. 2013)
Dhungel 2015 Parkinson's disease genes VPS35 and EIF4G1 interact genetically and converge on α-synuclein. (Dhungel et al. 2015)
Gerashchenko 2014 Translation inhibitors cause abnormalities in ribosome profiling experiments. (Gerashchenko et al. 2014)
Gerashchenko 2016 Ribonuclease selection for ribosome profiling. (Gerashchenko et al. 2016)
Gerashenko 2012 Ribosome profiles of elongating ribosomes from the yeast Saccharomyces cerevisiae carried out under control conditions (without oxidative stress) and at 5 and 30 minutes of oxidative stress (Gerashenko et al. 2012)
Guydosh 14 Dom34 rescues ribosomes in 3' untranslated regions. (Guydosh et al. 14)
Ingolia 2009 Ribosome profiles of elongating ribosomes from the yeast Saccharomyces cerevisiae carried out under both rich and starvation conditions (Ingolia et al. 2009)
Jungfleisch 2017 A novel translational control mechanism involving RNA structures within coding sequences. (Jungfleisch et al. 2017)
Lareau 2014 Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. (Lareau et al. 2014)
Nedialkova15 Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. (Nedialkova et al. 2015)
Nissley 2016 Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding (Nissley et al. 2016)
Pop 2014 Ribosome profiles of elongating ribosomes from wild type yeast and in mutants with altered tRNA levels in physiological conditions (Pop et al. 2014)
Schmidt16 The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. (Schmidt et al. 2016)
Sen 2015 Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. (Sen et al. 2015)
Sen 2016 eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. (Sen et al. 2016)
Subtelny 2014 Poly(A)-tail profiling reveals an embryonic switch in translational control. (Subtelny et al. 2014)
Thiaville 2016 Global translational impacts of the loss of the tRNA modification t6A in yeast. (Thiaville et al. 2016)
Yerlikaya_2015 Ribosome profilings of transcriptome and translatome in Saccharomyces cerevisiae (Yerlikaya et al. 2015)
Young 15 Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo. (Young et al. 15)
Zid 2014 Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. (Zid et al. 2014)
Zinshteyn 2013 Loss of a conserved tRNA anticodon modification perturbs cellular signaling. (Zinshteyn et al. 2013)
-   Elongating Ribosomes (Footprints)    
Global Aggregate Ribo-seq unique mappers from all studies
Albert 2014 Genetic influences on translation in yeast. (Albert et al. 2014)
Archer 2016 Dynamics of ribosome scanning and recycling revealed by translation complex profiling. (Archer et al. 2016)
Baudin-Baillieu 2014 Ribo-seq unique mappers from Sacchromyces cerevisiae [PSI+] and [psi-] strains (Baudin-Baillieu et al. 2014)
Beaupere17 CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes. (Beaupere et al. 2017)
Brar 2012 Ribo-seq unique mappers from the yeast Saccharomyces cerevisiae during meiosis from traditional timecourse, strain ndt80, strain A14201, strain gb15 and strain mata/a (Brar et al. 2012)
Cai 2013 Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. (Cai et al. 2013)
Dhungel 2015 Parkinson's disease genes VPS35 and EIF4G1 interact genetically and converge on α-synuclein. (Dhungel et al. 2015)
Gerashchenko 2014 Translation inhibitors cause abnormalities in ribosome profiling experiments. (Gerashchenko et al. 2014)
Gerashchenko 2016 Ribonuclease selection for ribosome profiling. (Gerashchenko et al. 2016)
Gerashenko 2012 Ribo-seq unique mappers from the yeast Saccharomyces cerevisiae carried out under control conditions (without oxidative stress) and at 5 and 30 minutes of oxidative stress (Gerashenko et al. 2012)
Guydosh 14 Dom34 rescues ribosomes in 3' untranslated regions. (Guydosh et al. 14)
Ingolia 2009 Ribo-seq unique mappers from the yeast Saccharomyces cerevisiae carried out under both rich and starved conditions (Ingolia et al. 2009)
Jungfleisch 2017 A novel translational control mechanism involving RNA structures within coding sequences. (Jungfleisch et al. 2017)
Lareau 2014 Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. (Lareau et al. 2014)
Nedialkova15 Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. (Nedialkova et al. 2015)
Nissley 2016 Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding (Nissley et al. 2016)
Pop 2014 Ribo-seq unique mappers from wild type yeast and in mutants with altered tRNA levels in physiological conditions (Pop et al. 2014)
Schmidt16 The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. (Schmidt et al. 2016)
Sen 2015 Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. (Sen et al. 2015)
Sen 2016 eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. (Sen et al. 2016)
Subtelny 2014 Poly(A)-tail profiling reveals an embryonic switch in translational control. (Subtelny et al. 2014)
Thiaville 2016 Global translational impacts of the loss of the tRNA modification t6A in yeast. (Thiaville et al. 2016)
Yerlikaya_2015 This track contains data from Ribosomal sequence experiments carried out by (Yerlikaya et al. 2015)
Young 15 Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo. (Young et al. 15)
Zid 2014 Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. (Zid et al. 2014)
Zinshteyn 2013 Loss of a conserved tRNA anticodon modification perturbs cellular signaling. (Zinshteyn et al. 2013)
-   mRNA-seq Reads    
Global aggregate mRNA-seq unique mappers from all studies
Albert 2014 Genetic influences on translation in yeast. (Albert et al. 2014)
Archer 2016 Dynamics of ribosome scanning and recycling revealed by translation complex profiling.(Archer et al. 2016)
Beaupere17 CAN1 Arginine Permease Deficiency Extends Yeast Replicative Lifespan via Translational Activation of Stress Response Genes. (Beaupere et al. 2017)
Brar 2012 mRNA-seq unique mappers from the yeast Saccharomyces cerevisiae during meiosis from traditional timecourse, strain ndt80, strain A14201, strain gb15 and strain mata/a (Brar et al. 2012)
Cai 2013 Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. (Cai et al. 2013)
Gerashenko 2012 mRNA-seq unique mappers from the yeast Saccharomyces cerevisiae carried out under control conditions (without oxidative stress) and at 5 and 30 minutes of oxidative stress (Gerashenko et al. 2012)
Guydosh 14 Dom34 rescues ribosomes in 3' untranslated regions. (Guydosh et al. 14)
Ingolia 2009 mRNA-seq unique mappers from the yeast Saccharomyces cerevisiae carried out under both rich and starved conditions (Ingolia et al. 2009)
Jungfleisch 2017 A novel translational control mechanism involving RNA structures within coding sequences. (Jungfleisch et al. 2017)
Nedialkova15 Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. (Nedialkova et al. 2015)
Pop 2014 mRNA-seq unique mappers from wild type yeast and in mutants with altered tRNA levels in physiological conditions (Pop et al. 2014)
Schmidt16 The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. (Schmidt et al. 2016)
Sen 2015 Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. (Sen et al. 2015)
Sen 2016 eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. (Sen et al. 2016)
Subtelny 2014 Poly(A)-tail profiling reveals an embryonic switch in translational control. (Subtelny et al. 2014)
Yerlikaya 2015 mRNA unique coverage profiling in S.cerevisiae cell (Yerlikaya et al. 2015)
Young 15 Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo. (Young et al. 15)
Zid 2014 Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. (Zid et al. 2014)
Zinshteyn 2013 Loss of a conserved tRNA anticodon modification perturbs cellular signaling. (Zinshteyn et al. 2013)
-   Annotation Tracks and External Data    
SGD Genes Protein-Coding Genes from Saccharomyces Genome Database
SGD Other Other Features from Saccharomyces Genome Database
Ensembl Genes Ensembl Genes
TIF-Seq Transcript Isoform Sequencing
Short Match Perfect Matches to Short Sequence (TATAWAAR)
Conservation 7 yeast Multiz Alignment & Conservation
Most Conserved PhastCons Conserved Elements, 7 yeast Multiz Alignment
Simple Repeats Simple Tandem Repeats by TRF