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Configure Tracks on UCSC Genome Browser: SARS-CoV-2 Jan. 2020/NC_045512.2 (wuhCor1)
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-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Kim IVT Cov Kim 2020 in-vitro-transcribed RNA seq + PCR: Nanopore coverage
ARTIC Primers ARTIC Oxford Nanopore sequencing primers
new RAPID Primers RAPID Oxford Nanopore sequencing primers
Crowd-Sourced Data Crowd-sourced data: annotations contributed via bit.ly/cov2annots
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
new 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
Transcriptome SARS-CoV-2 Trancriptome tracks
Protein Interact. Human Interacting Proteins from Gordon et al. (* = druggable)
PDB Structures Protein Data Bank (PDB) Sequence Matches
new 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
new PhyloCSF Genes PhyloCSF Genes - Curated conserved genes
Rangan RNA Rangan et al. RNA predictions
Rfam Rfam families
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   UniProt Protein Annotations    
Full Proteins UniProt full-length proteins
Protein Products UniProt Protein Products (Polypeptide Chains)
Highlights UniProt highlighted "Regions of Interest"
Signal Peptides UniProt Signal Peptides
Transmem. Domains UniProt Transmembrane Domains
Disulf. Bonds UniProt Disulfide Bonds
Protein Domains UniProt Domains
Glycosyl/Phosph. UniProt Amino Acid Glycosylation/Phosphorylation sites
Other Annot. UniProt Other Annotations
Structure UniProt Protein Primary/Secondary Structure Annotations
Repeats UniProt Repeats
Protease Cleavage Protease Cleavage Sites
-   Immunology    
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
-   Expression and Regulation    
Kim Transcripts Canonical SARS-CoV-2 Transcript Information from Kim et al. 2020
Kim RNA Brkpts Kim 2020 RNA-seq: Nanopore and MGISeq Breakpoints
Kim RNA Modif Kim et al. Nanopore RNA Modifications: gRNA S 3a E M 6 7a 7b 8 N
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)
new 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
new Human CoV Multiz Alignment and Conservation of 7 Strains of human coronavirus
-   Variation and Repeats    
new SARS-CoV-2 Phylogeny Phylogenetic tree and common variants from high-coverage sequences in GISAID
updated Nextstrain Clades Nextstrain year-letter clade designations (19A, 19B, 20A, etc.) from nextstrain.org/ncov
updated Nextstrn Old Clades Old (March 2020) Nextstrain clade designations (A1a, A2, etc.) from nextstrain.org/ncov
updated Nextstrain Variants Nextstrain/GISAID Sample Variants from nextstrain.org/ncov
new Microdeletions Microdeletions
updated Nextstrain Frequency Nextstrain Variants Alternate Allele Frequency
updated Nextstrain Parsimony Parsimony Scores for Nextstrain Variants and Phylogenetic Tree
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust