UCSC Genome Browser on SARS-CoV-2 Jan. 2020 (NC_045512.2) (wuhCor1)
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NC_045512v2:25,183-28,377 3,195 bp.   Quick start guide
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  Click on a feature for details. Shift+click+drag to zoom in. Click grey side bars for track options. Drag side bars or labels up or down to reorder tracks. Drag tracks left or right to new position. Press "?" for keyboard shortcuts. Use drop-down controls below and press refresh to alter tracks displayed.   move end
-   Custom Tracks
MEA Seccondary Structures Rangan Das 2020 with Pubmed and Rfam annotations
TRS (CUAAAC) [+purple/-teal]
TRS (CUAAAC) [+purple/-teal] - TRS COMPLEMENT (GUUUAG) [+mustard]
-   Mapping and Sequencing
Base Position
Nanopore coverage
ARTIC Primers V3
ARTIC Primers V4
ARTIC Primers V4.1
RAPID/Midnight Primers
Swift Primers
Crowd-Sourced Data
NEB VarSkip Primers
Addgene Plasmids
CRISPR Detection
GC Percent
Problematic Sites
RefSeq Acc
Restr Enzymes
RT-PCR Primers
Short Match
Blat Sequence
-   Genes and Gene Predictions
NCBI Genes
NCBI Proteins
Subgenomic Canonical
Subgenomic Breakpts
Subgenomic Observed
Subgenomic RNA Modif.
Protein Interact.
Weizman ORFs
PDB Structures
PDB Ligand Contacts
Genscan Genes
Nextstrain Genes
PhyloCSF Genes
-   UniProt Protein Annotations
Precurs. Proteins
Protein Alignments
Protein Products
Signal Peptides
Transmem. Domains
Disulf. Bonds
Protein Domains
Other Annot.
Protease Cleavage
-   Immunology
RBD Mut Bind
RBD Mut Expr
Antib Pept Array
S Antib Pept Array
Antibody Escape
CD8 Escape Muts
CD8 RosettaMHC
IEDB Predictions
Poran HLA I
Poran HLA II
T-React. Epitopes
Validated epitopes from IEDB
-   mRNA and EST
SHAPE Struct Pyle
icSHAPE RNA Struct
Rangan RNA
-   Expression and Regulation
CpG Islands
-   Comparative Genomics
44 Bat CoVs
119 Vertebrate CoVs
Human CoV
-   Variation and Repeats
Phylogeny: Public
Phylogeny: GISAID
updated Nextstrain Clades
updated Nextstrain Mutations
Intrahost SNPs
Nat. Selection (Pond)
Drug Resistance Mutations
Galaxy ENA mutations
updated Nextstrain Frequency
updated Nextstrain Parsimony
Pot. pathogenic indels
Predicted Resistance
Recomb. Breakpoints
Simple Repeats
Spike Mutations
new Variants of Concern
WM + SDust

For information about this browser and related resources, see COVID-19 Research at UCSC.

GISAID data displayed in the Genome Browser are subject to GISAID's Terms and Conditions. SARS-CoV-2 genome sequences and metadata are available for download from GISAID EpiCoV™.

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