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Configure Tracks on UCSC Genome Browser: SARS-CoV-2 Jan. 2020 (NC_045512.2) (wuhCor1)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Nanopore coverage Nanopore coverage of in-vitro-transcribed RNA seq + PCR, Kim et al 2020
ARTIC Primers V3 ARTIC V3 Oxford Nanopore sequencing primers
ARTIC Primers V4 ARTIC V4 Oxford Nanopore sequencing primers
ARTIC Primers V4.1 ARTIC V4.1 Oxford Nanopore sequencing primers
RAPID/Midnight Primers RAPID/Midnight 1200bp amplicon Oxford Nanopore sequencing primers
Swift Primers Swift BioSciences sequencing primers
Crowd-Sourced Data Crowd-sourced data: annotations contributed via bit.ly/cov2annots
NEB VarSkip Primers New England Biolabs (NEB) VarSkip Primers
Cas13 CRISPR Cas13 CRISPR targets
Addgene Plasmids Addgene Plasmid Sequences alignable to the Genome
Assembly Assembly from Fragments
CRISPR Detection CRISPR Detection Guides
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
Problematic Sites Problematic sites where masking or caution are recommended for analysis
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
RT-PCR Primers RT-PCR Detection Kit Primer Sets
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Predictions    
NCBI Genes NCBI Genes from NC_045512.2
NCBI Proteins NCBI Proteins: annotated mature peptide products
Subgenomic Canonical Canonical Subgenomic Transcripts
Subgenomic Breakpts Subgenomic Transcript Breakpoints from Kim et al 2020: Nanopore and MGISeq
Subgenomic Observed Subgenomic Transcripts found in long-read sequences by Kim et al. 2020
Subgenomic RNA Modif. Subgenomic RNA Modifications from Kim et al. 2020: gRNA S 3a E M 6 7a 7b 8 N
Protein Interact. Human Interacting Proteins from Gordon et al. (* = druggable)
Weizman ORFs New ORFs based on RNA-seq and Ribo-seq by the Weizman Institute
     Vero6 24hpi     Vero6 24hpi Ribo-seq and RNA-seq
     Vero6 5hpi     Vero6 5hpi Ribo-seq and RNA-seq
     Calu3 7hpi     Calu3 7hpi Ribo-seq and RNA-seq
     ORF predictions     Weizman ORF predictions
PDB Structures Protein Data Bank (PDB) Sequence Matches
PDB Ligand Contacts Potential contact residues in PDB structures of viral proteins
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
Genscan Genes Genscan Gene Predictions
Nextstrain Genes Genes annotated by nextstrain.org/ncov
PhyloCSF Genes PhyloCSF Genes - Curated conserved genes
-   UniProt Protein Annotations    
Precurs. Proteins UniProt Precursor Proteins (before cleavage into protein products)
Protein Alignments UCSC alignment of full-length SwissProt proteins to genome
Protein Products UniProt Protein Products (Polypeptide Chains, after cleavage)
Highlights UniProt highlighted "Regions of Interest"
Signal Peptides UniProt Signal Peptides
Extracellular UniProt Extracellular Domain
Transmem. Domains UniProt Transmembrane Domains
Cytoplasmic UniProt Cytoplasmic Domains
Disulf. Bonds UniProt Disulfide Bonds
Protein Domains UniProt Domains
Glycosyl/Phosph. UniProt Amino Acid Glycosylation/Phosphorylation sites
Mutations UniProt Amino Acid Mutations
Other Annot. UniProt Other Annotations
Structure UniProt Protein Primary/Secondary Structure Annotations
Repeats UniProt Repeats
Protease Cleavage Protease Cleavage Sites
-   Immunology    
RBD Mut Bind S RBD Deep Mutational Scanning: ACE2 Binding (Jesse Bloom's Group)
RBD Mut Expr S RBD Deep Mutational Scanning: Expression (Jesse Bloom's Group)
Antib Pept Array Antibody Proteome Peptide Binding Microarray Raw Data from Wang et al, ACS 2020, Xiaobo Yu group, NCPSB Beijing
     IgM Z-score - early COVID-19 patients     Proteome Peptide Microarray - IgM - early COVID-19 patients
     IgG Z-score- early COVID-19 patients     Proteome Peptide Microarray - IgG - early COVID-19 patients
     Antib Pept Array Sum (IgM)     Antibody Proteome Peptide Binding Microarray, Wang et al 2020 - IgM, Covid - Sum of scores per nucleotide
     Antib Pept Array Sum (IgG)     Antibody Proteome Peptide Binding Microarray, Wang et al 2020 - IgG, Covid - Sum of scores per nucleotide
S Antib Pept Array S Protein Antibody Peptide Binding Microarray from Li et al, Cell & Mol Imm 2020, Sheng-ce Tao group, Jiao Tung Univ.
     S-PBM: IgM Response Frequency     S Protein Antibody Peptide Binding Microarray - IgM - Response Frequency
     S-PBM: IgG Response Frequency     S Protein Antibody Peptide Binding Microarray - IgG - Response Frequency
     S-PBM IgM     S Protein Antibody Peptide Binding Microarray - IgM - Sheng-ce Tao group, Jiao Tung Univ.
     S-PBM IgG     S Protein Antibody Peptide Binding Microarray - IgG - Sheng-ce Tao group, Jiao Tung Univ.
Antibody Escape Escape from serum or monoclonal antibodies: Whelan, Bloom and Rappuoli groups
     McCoy Escape     McCoy lab: S Mutation impact on neutralization by serum and mAbs
     Rappuoli Serum Escape     Rappuoli lab: S Mutations that lead to escape from neutralizing antibodies from plasma of a single patient
     Whelan 21 Ab     Whelan lab: RBD Mutations that lead to escape from 21 monoclonal antibodies (click to show mutation details)
     Bloom Total Escape     Bloom Lab: S RBD-mutation antibody escape - total escape score per amino acid - 13 MABs and serum from 11 patients (A-K)
     Bloom Max Escape     Bloom Lab: S RBD-mutation antibody escape - maximum escape score per amino acid - 13 MABs and serum from 11 patients (A-K)
     Bloom Strong Mutations     Bloom Lab: Strong S RBD-mutation antibody escape - positions with max score > 0.18 - shading = number of samples where found
     Bloom MAB Average     Bloom Lab: S RBD-mutation monoclonal antibody escape - average score across all 13 MAB samples
     Bloom Serum Average     Bloom Lab: S RBD-mutation patient serum antibody escape - average score across serum samples (patients A-K)
CD8 Escape Muts T-Cell MHCI CD8+ Escape Mutations from Agerer et al. Sci Immun 2020
CD8 RosettaMHC CD8 Epitopes predicted by NetMHC and Rosetta
IEDB Predictions IEDB-Predicted Epitopes from Grifoni et al 2020
Poran HLA I RECON HLA-I epitopes
Poran HLA II RECON HLA-II epitopes
T-React. Epitopes T-cell reactive epitopes in patients and donors
Vaccines COVID Vaccines BioNTech/Pfizer BNT-162b2 and Moderna mRNA-1273
Validated epitopes from IEDB Validated epitopes from IEDB
-   mRNA and EST    
SHAPE Struct Pyle RNA SHAPE Structure from the Pyle group
icSHAPE RNA Struct icSHAPE RNA Structure
Rangan RNA Rangan et al. RNA predictions
Rfam Rfam families
-   Expression and Regulation    
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
-   Comparative Genomics    
44 Bat CoVs Multiz Alignment & Conservation (44 Strains with bats as hosts)
119 Vertebrate CoVs Multiz Alignment & Conservation (119 strains: strains with vertebrate hosts and human SARS-Cov2)
PhyloCSF PhyloCSF
     Smoothed PhyloCSF-3     Smoothed PhyloCSF Strand - Frame 3
     Smoothed PhyloCSF-2     Smoothed PhyloCSF Strand - Frame 2
     Smoothed PhyloCSF-1     Smoothed PhyloCSF Strand - Frame 1
     Smoothed PhyloCSF+3     Smoothed PhyloCSF Strand + Frame 3
     Smoothed PhyloCSF+2     Smoothed PhyloCSF Strand + Frame 2
     Smoothed PhyloCSF+1     Smoothed PhyloCSF Strand + Frame 1
     PhyloCSF Power     Relative branch length of local alignment, a measure of PhyloCSF statistical power
Human CoV Multiz Alignment and Conservation of 7 Strains of human coronavirus
-   Variation and Repeats    
Phylogeny: Public Phylogenetic Tree and Nucleotide Substitution Mutations in Sequences in Public Databases
Phylogeny: GISAID Phylogenetic Tree and Nucleotide Substitution Mutations in High-coverage Sequences in GISAID EpiCoV TM
updated Nextstrain Clades Nextstrain year-letter clade designations (19A, 19B, 20A, etc.)
updated Nextstrain Mutations Nextstrain Subset of GISAID EpiCoV TM Sample Mutations
Intrahost SNPs Intrahost SNP patient data from Todd Treangen's group
Nat. Selection (Pond) Natural selection analysis from Sergei Pond's research group
Drug Resistance Mutations Mutations that confer drug resistance (Anna Niewiadomska, BV-BRC)
Galaxy ENA mutations GalaxyProject surveillance of SARS-CoV-2 mutations through consistent processing of public raw sequencing data
     Galaxy ENA mutations in top lineages - three quarters ago     Most frequent lineages of three quarters ago
     Galaxy ENA mutations in top lineages - two quarters ago     Most frequent lineages of two quarters ago
     Galaxy ENA mutations in top lineages - a quarter ago     Most frequent lineages of a quarter ago
     Galaxy ENA mutations in top lineages - current quarter     Most frequent lineages of current quarter
Microdeletions Microdeletions in GISAID sequences
updated Nextstrain Frequency Nextstrain Mutations Alternate Allele Frequency
updated Nextstrain Parsimony Parsimony Scores for Nextstrain Mutations and Phylogenetic Tree
Pot. pathogenic indels Potential pathogenic insertions and deletions from Gussow et al, PNAS 2020
Predicted Resistance Mutations that may confer drug resistance - from Coronavirus3d.org (label: count of GISAID sequences with mutation, Feb 2022)
Recomb. Breakpoints Recombination Breakpoints from Thurakia et al 2022
Simple Repeats Simple Tandem Repeats by TRF
Spike Mutations Spike protein mutations from community annotation (Feb 2021)
new Variants of Concern Mutations in Variants of Concern (VOC), Interest (VOI), or Under Monitoring (VUM) (configure to show more lineages)
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
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