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Configure Tracks on GWIPS-viz Genome Browser: Human Dec. 2013 (GRCh38/hg38)
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-   Small Ribosomal Subunits (Footprints)    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
HEK: Wagner20 Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes (Wagner et al. 2020)
-   Initiating Ribosomes (P-site)    
Global Aggregate initiating Ribosome Profiles from all studies.
BJ/MCF10A:Ji 2015 Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins (Ji et al. 2015)
HCT116: Fijalkowska17 eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. (Fijalkowska et al. 2017)
HCT116:Crappe 2015 PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. (Crappe et al. 2015)
HEK293: Gao14 Quantitative profiling of initiating ribosomes in vivo (Xiangwei et al. 2014)
HEK: Zhang17 Genome-wide identification and differential analysis of translational initiation. (Zhang et al. 2017)
iPSC: Chen20 Pervasive functional translation of noncanonical human open reading frames (Chen et al. 2020)
Jurkat: Gawron 2016 Positional proteomics reveals differences in N-terminal proteoform stability. (Gawron et al. 2016)
LCL :Raj 2016 Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. (Raj et al. 2016)
-   Elongating Ribosomes (A-site)    
Global Aggregate Ribosome Profiles from all studies.
BJ/MCF10A:Ji 2015 Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins (Ji et al. 2015)
Blood: Mills16 Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets. (Mills et al. 2016)
Erythroid: Khajuria18 Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. (Khajuria et al. 2018)
Fibroblast: Tirosh 2015 The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions (Tirosh et al. 2015)
Fibroblast:Xu 2016 Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. (Xu et al. 2016)
Flp-In T-REx-293: Malecki17 The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A) (Malecki et al. 2017)
HAP1: Jakobsson17 Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA trans... (Jakobsson et al. 2017)
HCT116: Fijalkowska17 eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. (Fijalkowska et al. 2017)
HCT116:Crappe 2015 PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. (Crappe et al. 2015)
HEK293: Clamer18 Active Ribosome Profiling with RiboLace. (Clamer et al. 2018)
HEK293: Gao14 Quantitative profiling of initiating ribosomes in vivo (Xiangwei et al. 2014)
HEK293: Iwasaki19 The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. (Iwasaki et al. 2019)
HEK: Andreev15 Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. (Andreev et al. 2015)
HEK: Calviello 2016 Detecting actively translated open reading frames in ribosome profiling data. (Calviello et al. 2016)
HEK: Ingolia12 The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. (Ingolia et al. 2012)
HEK: Iwasaki 2016 Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. (Iwasaki et al. 2016)
HEK: Oh16 Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. (Oh et al. 2016)
HEK: Park17 mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4. (Park et al. 2017)
HEK: Sidrauski 2015 The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly (Sidrauski et al. 2015)
HEK: Wagner20 Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes (Wagner et al. 2020)
HEK: Zhang17 Genome-wide identification and differential analysis of translational initiation. (Zhang et al. 2017)
HeLa :Park 2016 Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. (Park et al. 2016)
HeLa: Arango18 Acetylation of Cytidine in mRNA Promotes Translation Efficiency. (Arango et al. 2018)
HeLa: Niu 2013 N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. (Niu et al. 2013)
HeLa: Shi17 YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. (Shi et al. 2017)
HeLa: Yoon 2014 PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. (Yoon et al. 2014)
HeLa:Zur 2016 Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. (Zur et al. 2016)
hESC: Werner 2015 Cell fate determination by ubiquitin-dependent regulation of translation (Werner et al. 2015)
hTERT-RPE-1: Haas20 PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of mult... (Haas et al. 2020)
iPSC: Chen20 Pervasive functional translation of noncanonical human open reading frames (Chen et al. 2020)
Jurkat: Gawron 2016 Positional proteomics reveals differences in N-terminal proteoform stability. (Gawron et al. 2016)
KOPT-K1: Wolfe 2014 RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. (Wolfe et al. 2014)
LCL: Battle 2015 Impact of Regulatory Variation from RNA to Protein (Battle et al. 2015)
LCL: Cenik 2015 Ribosome Profiling and RNA sequencing experiments from human lymphoblastoid cells (Cenik et al. 2015)
Lymphocytes: Reid 2015 Simple and inexpensive ribosome profiling analysis of mRNA translation. (Reid et al. 2015)
MCF10A-ER-Src: Gameiro18 Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis. (Gameiro et al. 2018)
MCF7: Lauria18 riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. (Lauria et al. 2018)
MCF7: LoayzaPuch16 Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. (LoayzaPuch et al. 2016)
MDA-MB-231: Rubio 2014 Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. (Rubio et al. 2014)
Monocytes :Su 2015 Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. (Su et al. 2015)
Muscle:Wein 2014 Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. (Wein et al. 2014)
Myeloma:Wiita 2013 Global cellular response to chemotherapy-induced apoptosis. (Wiita et al. 2013)
RPE1: Tanenbaum 2015 Regulation of mRNA translation during mitosis (Tanenbaum et al. 2015)
U20S :Guo 2014 Expanded identification and characterization of mammalian circular RNAs. (Guo et al. 2014)
U2OS: Elkon 2015 Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. (Elkon et al. 2015)
U2OS: Jang 2015 Ribosome profiling reveals an important role for translational control in circadian gene expression (Jang et al. 2015)
-   Elongating Ribosomes (Footprints)    
Global Aggregate Ribo-seq coverage data from all studies.
BJ/MCF10A:Ji 2015 Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins (Ji et al. 2015)
Blood: Mills16 Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets. (Mills et al. 2016)
Erythroid: Khajuria18 Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. (Khajuria et al. 2018)
Fibroblast: Tirosh 2015 The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions (Tirosh et al. 2015)
Fibroblast:Xu 2016 Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. (Xu et al. 2016)
Flp-In T-REx-293: Malecki17 The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A) (Malecki et al. 2017)
HAP1: Jakobsson17 Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA trans... (Jakobsson et al. 2017)
HCT116: Fijalkowska17 eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. (Fijalkowska et al. 2017)
HCT116:Crappe 2015 PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. (Crappe et al. 2015)
HEK293: Clamer18 Active Ribosome Profiling with RiboLace. (Clamer et al. 2018)
HEK293: Gao14 Quantitative profiling of initiating ribosomes in vivo (Xiangwei et al. 2014)
HEK293: Iwasaki19 The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. (Iwasaki et al. 2019)
HEK: Andreev15 Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. (Andreev et al. 2015)
HEK: Calviello 2016 Detecting actively translated open reading frames in ribosome profiling data. (Calviello et al. 2016)
HEK: Ingolia12 The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. (Ingolia et al. 2012)
HEK: Iwasaki 2016 Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. (Iwasaki et al. 2016)
HEK: Oh16 Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. (Oh et al. 2016)
HEK: Park17 mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4. (Park et al. 2017)
HEK: Sidrauski 2015 The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly (Sidrauski et al. 2015)
HEK: Wagner20 Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes (Wagner et al. 2020)
HEK: Zhang17 Genome-wide identification and differential analysis of translational initiation. (Zhang et al. 2017)
HeLa :Park 2016 Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. (Park et al. 2016)
HeLa: Arango18 Acetylation of Cytidine in mRNA Promotes Translation Efficiency. (Arango et al. 2018)
HeLa: Niu 2013 N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. (Niu et al. 2013)
HeLa: Shi17 YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. (Shi et al. 2017)
HeLa: Yoon 2014 PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. (Yoon et al. 2014)
HeLa:Zur 2016 Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. (Zur et al. 2016)
hESC: Werner 2015 Cell fate determination by ubiquitin-dependent regulation of translation (Werner et al. 2015)
hTERT-RPE-1: Haas20 PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of mult... (Haas et al. 2020)
iPSC: Chen20 Pervasive functional translation of noncanonical human open reading frames (Chen et al. 2020)
Jurkat: Gawron 2016 Positional proteomics reveals differences in N-terminal proteoform stability. (Gawron et al. 2016)
KOPT-K1: Wolfe 2014 RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. (Wolfe et al. 2014)
LCL :Raj 2016 Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. (Raj et al. 2016)
LCL: Battle 2015 Impact of Regulatory Variation from RNA to Protein (Battle et al. 2015)
LCL: Cenik 2015 Ribosome Profiling experiments from human lymphoblastoid cells (Cenik et al. 2015)
Lymphocytes: Reid 2015 Simple and inexpensive ribosome profiling analysis of mRNA translation. (Reid et al. 2015)
MCF10A-ER-Src: Gameiro18 Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis. (Gameiro et al. 2018)
MCF7: Lauria18 riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. (Lauria et al. 2018)
MCF7: LoayzaPuch16 Tumour-specific proline vulnerability uncovered by differential ribosome codon reading. (LoayzaPuch et al. 2016)
MDA-MB-231: Rubio 2014 Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. (Rubio et al. 2014)
Monocytes :Su 2015 Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. (Su et al. 2015)
Muscle:Wein 2014 Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. (Wein et al. 2014)
Myeloma:Wiita 2013 Global cellular response to chemotherapy-induced apoptosis. (Wiita et al. 2013)
RPE1: Tanenbaum 2015 Regulation of mRNA translation during mitosis (Tanenbaum et al. 2015)
U20S :Guo 2014 Expanded identification and characterization of mammalian circular RNAs. (Guo et al. 2014)
U2OS: Elkon 2015 Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. (Elkon et al. 2015)
U2OS: Jang 2015 Ribosome profiling reveals an important role for translational control in circadian gene expression (Jang et al. 2015)
-   mRNA-seq Reads    
Global Aggregate mRNA-seq coverage data from all studies.
BJ/MCF10A:Ji 2015 Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins (Ji et al. 2015)
Erythroid: Khajuria18 Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. (Khajuria et al. 2018)
Fibroblast: Tirosh 2015 The transcription and translation landscapes during human cytomegalovirus infection reveal novel host-pathogen interactions (Tirosh et al. 2015)
Fibroblast:Xu 2016 Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. (Xu et al. 2016)
HAP1: Jakobsson17 Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA trans... (Jakobsson et al. 2017)
HCT116: Fijalkowska17 eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. (Fijalkowska et al. 2017)
HEK293: Gao14 Quantitative profiling of initiating ribosomes in vivo (Xiangwei et al. 2014)
HEK: Andreev15 Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. (Andreev et al. 2015)
HEK: Iwasaki 2016 Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. (Iwasaki et al. 2016)
HEK: Oh16 Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. (Oh et al. 2016)
HEK: Park17 mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4. (Park et al. 2017)
HEK: Sidrauski 2015 The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly (Sidrauski et al. 2015)
HEK: Wagner20 Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes (Wagner et al. 2020)
HeLa :Park 2016 Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. (Park et al. 2016)
HeLa: Arango18 Acetylation of Cytidine in mRNA Promotes Translation Efficiency. (Arango et al. 2018)
HeLa: Niu 2013 N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. (Niu et al. 2013)
HeLa: Shi17 YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. (Shi et al. 2017)
HeLa:Zur 2016 Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. (Zur et al. 2016)
hESC: Werner 2015 Cell fate determination by ubiquitin-dependent regulation of translation (Werner et al. 2015)
hTERT-RPE-1: Haas20 PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of mult... (Haas et al. 2020)
iPSC: Chen20 Pervasive functional translation of noncanonical human open reading frames (Chen et al. 2020)
KOPT-K1: Wolfe 2014 RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. (Wolfe et al. 2014)
LCL: Battle 2015 Impact of regulatory variation from RNA to protein (Battle et al. 2015)
LCL: Cenik 2015 RNA sequencing experiments from human lymphoblastoid cells (Cenik et al. 2015)
MCF10A-ER-Src: Gameiro18 Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis. (Gameiro et al. 2018)
MCF7: Lauria18 riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. (Lauria et al. 2018)
MDA-MB-231: Rubio 2014 Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. (Rubio et al. 2014)
Monocytes :Su 2015 Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation. (Su et al. 2015)
Muscle:Wein 2014 Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. (Wein et al. 2014)
Myeloma:Wiita 2013 Global cellular response to chemotherapy-induced apoptosis. (Wiita et al. 2013)
RPE1: Tanenbaum 2015 Regulation of mRNA translation during mitosis (Tanenbaum et al. 2015)
U20S :Guo 2014 Expanded identification and characterization of mammalian circular RNAs. (Guo et al. 2014)
U2OS: Elkon 2015 Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. (Elkon et al. 2015)
U2OS: Jang 2015 Ribosome profiling reveals an important role for translational control in circadian gene expression (Jang et al. 2015)
-   Mapping and Sequencing    
Short Match Perfect Matches to Short Sequence ()
-   Annotation Tracks and External Data    
Cons Primates Primates Multiz Alignment & Conservation (20 Species)
Conservation Multiz Alignment & Conservation (7 Species)
phyloP 100way 100 vertebrates Basewise Conservation by PhyloP (phyloP100way)
NCBI RefSeq RefSeq gene predictions from NCBI
RefSeq Genes RefSeq Genes
CCDS Consensus CDS
GENCODE (Ensembl) GENCODE Gene Annotations (Ensembl)
     GENCODE V22 (Ensembl 79)     Gene Annotations from GENCODE Version 22 (Ensembl 79)
     GENCODE V20 (Ensembl 76)     Gene Annotations from GENCODE Version 20 (Ensembl 76)
     All GENCODE V28     All GENCODE annotations from V28 (Ensembl 92)
     All GENCODE V25     All GENCODE transcripts including comprehensive set V25
     All GENCODE V41     All GENCODE annotations from V41 (Ensembl 107)
MANE v1.0 NCBI RefSeq and Ensembl transcripts from the MANE Project (v1.0)
Mappability Hoffman Lab Umap and Bismap Mappability
     Bismap     Single-read and multi-read mappability after bisulfite conversion
     Umap     Single-read and multi-read mappability by Umap