UCSC Genome Browser on SARS-CoV-2 Jan. 2020/NC_045512.2 Assembly (wuhCor1)
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NC_045512v2:25,183-28,377 3,195 bp.
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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
Kim IVT Cov
ARTIC Primers
RAPID/Midnight Primers
new Swift Primers
Crowd-Sourced Data
Cas13 CRISPR
Addgene Plasmids
Assembly
CRISPR Detection
Gap
GC Percent
INSDC
Problematic Sites
RefSeq Acc
Restr Enzymes
RT-PCR Primers
Short Match
Blat Sequence
-   Genes and Gene Predictions
NCBI Genes
NCBI Proteins
Transcriptome Kim
Protein Interact.
Weizman ORFs...
PDB Structures
PDB Ligand Contacts
AUGUSTUS
Genscan Genes
Nextstrain Genes
PhyloCSF Genes
-   UniProt Protein Annotations
Precurs. Proteins
Protein Alignments
Protein Products
Highlights
Signal Peptides
Extracellular
Transmem. Domains
Cytoplasmic
Disulf. Bonds
Protein Domains
Glycosyl/Phosph.
Mutations
Other Annot.
Structure
Repeats
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
new Vaccines
Validated epitopes from IEDB
-   mRNA and EST
SHAPE Struct Pyle
icSHAPE RNA Struct
Rangan RNA
Rfam
-   Expression and Regulation
Kim Transcripts
Kim RNA Brkpts
Kim RNA Modific.
CpG Islands...
-   Comparative Genomics
44 Bat CoVs
119 Vertebrate CoVs
PhyloCSF...
Human CoV
-   Variation and Repeats
Phylogeny: Public
Phylogeny: GISAID
updated Nextstrain Clades
updated Nextstrain Mutations
Intrahost SNPs
Natural Selection
B.1.1.7 in USA
Microdeletions
updated Nextstrain Frequency
updated Nextstrain Parsimony
Pot. pathogenic indels
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™.