SARS-CoV-2 (COVID-19) Genome

Complete genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate Wuhan-Hu-1, also known as COVID-19.
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Explore Over 2.7k Plasmids: Coronavirus Resources | More Plasmid Sets
No matches
25,000 20,000 15,000 10,000 5000 End (29,903) PvuI (29,753) ORF10 StuI (29,528) PspFI (29,202) BseYI (29,198) AbsI - XhoI - PspXI - PaeR7I (28,473) BsrBI (28,436) ORF8 ORF6 AgeI - SgrAI (26,751) BspEI (26,149) BamHI (25,313) SwaI (25,140) NaeI (15,960) NgoMIV (15,958) SacI (15,102) Eco53kI (15,100) PacI (8586) PmeI (6747) SmaI (4254) XmaI - TspMI (4252) BglI (846) PluTI (678) SfoI (676) NarI - BsaHI (675) KasI (674) NruI (336) TaqII (268) Start (0) 5' UTR orf1ab S ORF3a E M ORF7a N 3' UTR orf1ab stem loop mature peptide mature peptide mature peptide mature peptide ORF7b stem loop mature peptide mat... mature peptide mature peptide mature peptide mature peptide stem loop mature peptide stem loop SARS-CoV-2 (COVID-19) Genome 29,903 bp
End  (29,903)
0 sites
PvuI  (29,753)
1 site
C G A T C G G C T A G C
StuI  (29,528)
1 site
A G G C C T T C C G G A
PspFI  (29,202)
1 site
C C C A G C G G G T C G
BseYI  (29,198)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its electrophoretic mobility.
AbsI  (28,473)
1 site
C C T C G A G G G G A G C T C C
XhoI  (28,473)
1 site
C T C G A G G A G C T C
PspXI  (28,473)
1 site
V C T C G A G B B G A G C T C V
PaeR7I  (28,473)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
BsrBI  (28,436)
1 site
C C G C T C G G C G A G

This recognition sequence is asymmetric, so ligating blunt ends generated by BsrBI will not always regenerate a BsrBI site.
BsrBI is typically used at 37°C, but can be used at temperatures up to 50°C.
AgeI  (26,751)
1 site
A C C G G T T G G C C A
SgrAI  (26,751)
1 site
C R C C G G Y G G Y G G C C R C

Efficient cleavage requires at least two copies of the SgrAI recognition sequence.
BspEI  (26,149)
1 site
T C C G G A A G G C C T
BamHI  (25,313)
1 site
G G A T C C C C T A G G

After cleavage, BamHI-HF® (but not the original BamHI) can remain bound to DNA and alter its electrophoretic mobility.
SwaI  (25,140)
1 site
A T T T A A A T T A A A T T T A

SwaI is typically used at 25°C, but is 50% active at 37°C.
NaeI  (15,960)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NaeI recognition sequence.
NgoMIV  (15,958)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
SacI  (15,102)
1 site
G A G C T C C T C G A G
Eco53kI  (15,100)
1 site
G A G C T C C T C G A G
PacI  (8586)
1 site
T T A A T T A A A A T T A A T T
PmeI  (6747)
1 site
G T T T A A A C C A A A T T T G
SmaI  (4254)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
XmaI  (4252)
1 site
C C C G G G G G G C C C

Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
TspMI  (4252)
1 site
C C C G G G G G G C C C
BglI  (846)
1 site
G C C N N N N N G G C C G G N N N N N C C G

Sticky ends from different BglI sites may not be compatible.
PluTI  (678)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the PluTI recognition sequence.
SfoI  (676)
1 site
G G C G C C C C G C G G
NarI  (675)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the NarI recognition sequence.
BsaHI  (675)
1 site
G R C G Y C C Y G C R G

BsaHI is typically used at 37°C, but is even more active at 60°C.
KasI  (674)
1 site
G G C G C C C C G C G G
NruI  (336)
1 site
T C G C G A A G C G C T
TaqII  (268)
1 site
G A C C G A ( N ) 9 N N C T G G C T ( N ) 9

Sticky ends from different TaqII sites may not be compatible.
Start  (0)
0 sites
5' UTR
1 .. 265  =  265 bp
5' UTR
1 .. 265  =  265 bp
orf1ab
266 .. 21,555  =  21,290 bp
7096 amino acids  =  794.1 kDa
2 segments
   Segment 1:  
   266 .. 13,468  =  13,203 bp
   4401 amino acids  =  489.6 kDa
Product: orf1ab polyprotein
pp1ab; translated by -1 ribosomal frameshift
orf1ab
266 .. 21,555  =  21,290 bp
7096 amino acids  =  794.1 kDa
2 segments
   Segment 2:  
   13,468 .. 21,555  =  8088 bp
   2695 amino acids  =  304.5 kDa
Product: orf1ab polyprotein
pp1ab; translated by -1 ribosomal frameshift
orf1ab
266 .. 21,555  =  21,290 bp
7096 amino acids  =  794.1 kDa
2 segments
Product: orf1ab polyprotein
pp1ab; translated by -1 ribosomal frameshift
S
21,563 .. 25,384  =  3822 bp
1273 amino acids  =  141.2 kDa
Product: surface glycoprotein
structural protein; spike protein
S
21,563 .. 25,384  =  3822 bp
1273 amino acids  =  141.2 kDa
Product: surface glycoprotein
structural protein; spike protein
ORF3a
25,393 .. 26,220  =  828 bp
275 amino acids  =  31.1 kDa
Product: ORF3a protein
ORF3a
25,393 .. 26,220  =  828 bp
275 amino acids  =  31.1 kDa
Product: ORF3a protein
E
26,245 .. 26,472  =  228 bp
75 amino acids  =  8.4 kDa
Product: envelope protein
ORF4; structural protein; E protein
E
26,245 .. 26,472  =  228 bp
75 amino acids  =  8.4 kDa
Product: envelope protein
ORF4; structural protein; E protein
M
26,523 .. 27,191  =  669 bp
222 amino acids  =  25.1 kDa
Product: membrane glycoprotein
ORF5; structural protein
M
26,523 .. 27,191  =  669 bp
222 amino acids  =  25.1 kDa
Product: membrane glycoprotein
ORF5; structural protein
ORF6
27,202 .. 27,387  =  186 bp
61 amino acids  =  7.3 kDa
Product: ORF6 protein
ORF6
27,202 .. 27,387  =  186 bp
61 amino acids  =  7.3 kDa
Product: ORF6 protein
ORF7a
27,394 .. 27,759  =  366 bp
121 amino acids  =  13.7 kDa
Product: ORF7a protein
ORF7a
27,394 .. 27,759  =  366 bp
121 amino acids  =  13.7 kDa
Product: ORF7a protein
ORF8
27,894 .. 28,259  =  366 bp
121 amino acids  =  13.8 kDa
Product: ORF8 protein
ORF8
27,894 .. 28,259  =  366 bp
121 amino acids  =  13.8 kDa
Product: ORF8 protein
N
28,274 .. 29,533  =  1260 bp
419 amino acids  =  45.6 kDa
Product: nucleocapsid phosphoprotein
ORF9; structural protein
N
28,274 .. 29,533  =  1260 bp
419 amino acids  =  45.6 kDa
Product: nucleocapsid phosphoprotein
ORF9; structural protein
ORF10
29,558 .. 29,674  =  117 bp
38 amino acids  =  4.4 kDa
Product: ORF10 protein
ORF10
29,558 .. 29,674  =  117 bp
38 amino acids  =  4.4 kDa
Product: ORF10 protein
3' UTR
29,675 .. 29,903  =  229 bp
3' UTR
29,675 .. 29,903  =  229 bp
orf1ab
266 .. 13,483  =  13,218 bp
4405 amino acids  =  490.0 kDa
Product: orf1a polyprotein
pp1a
orf1ab
266 .. 13,483  =  13,218 bp
4405 amino acids  =  490.0 kDa
Product: orf1a polyprotein
pp1a
stem loop
13,488 .. 13,542  =  55 bp
Function: Coronavirus frameshifting stimulation element stem-loop 2
stem loop
13,488 .. 13,542  =  55 bp
Function: Coronavirus frameshifting stimulation element stem-loop 2
mature peptide
16,237 .. 18,039  =  1803 bp
Product: helicase
nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase; produced by pp1ab only
/protein_id=YP_009725308.1
mature peptide
16,237 .. 18,039  =  1803 bp
Product: helicase
nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase; produced by pp1ab only
/protein_id=YP_009725308.1
mature peptide
18,040 .. 19,620  =  1581 bp
Product: 3'-to-5' exonuclease
nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab only
/protein_id=YP_009725309.1
mature peptide
18,040 .. 19,620  =  1581 bp
Product: 3'-to-5' exonuclease
nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab only
/protein_id=YP_009725309.1
mature peptide
19,621 .. 20,658  =  1038 bp
Product: endoRNAse
nsp15-A1 and nsp15B-NendoU; produced by pp1ab only
/protein_id=YP_009725310.1
mature peptide
19,621 .. 20,658  =  1038 bp
Product: endoRNAse
nsp15-A1 and nsp15B-NendoU; produced by pp1ab only
/protein_id=YP_009725310.1
mature peptide
20,659 .. 21,552  =  894 bp
Product: 2'-O-ribose methyltransferase
nsp16_OMT; 2'-o-MT; produced by pp1ab only
/protein_id=YP_009725311.1
mature peptide
20,659 .. 21,552  =  894 bp
Product: 2'-O-ribose methyltransferase
nsp16_OMT; 2'-o-MT; produced by pp1ab only
/protein_id=YP_009725311.1
ORF7b
27,756 .. 27,887  =  132 bp
43 amino acids  =  5.2 kDa
Product: ORF7b
ORF7b
27,756 .. 27,887  =  132 bp
43 amino acids  =  5.2 kDa
Product: ORF7b
stem loop
29,609 .. 29,644  =  36 bp
Function: Coronavirus 3' UTR pseudoknot stem-loop 1
stem loop
29,609 .. 29,644  =  36 bp
Function: Coronavirus 3' UTR pseudoknot stem-loop 1
stem loop
29,728 .. 29,768  =  41 bp
Function: Coronavirus 3' stem-loop II-like motif (s2m)
basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair, but the homologous positions form a highly conserved C:G basepair in other viruses, including SARS (NC_004718.3)
stem loop
29,728 .. 29,768  =  41 bp
Function: Coronavirus 3' stem-loop II-like motif (s2m)
basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair, but the homologous positions form a highly conserved C:G basepair in other viruses, including SARS (NC_004718.3)
mature peptide
266 .. 805  =  540 bp
Product: leader protein
nsp1; produced by both pp1a and pp1ab
/protein_id=YP_009725297.1
mature peptide
266 .. 805  =  540 bp
Product: leader protein
nsp1; produced by both pp1a and pp1ab
/protein_id=YP_009725297.1
mature peptide
806 .. 2719  =  1914 bp
Product: nsp2
produced by both pp1a and pp1ab
/protein_id=YP_009725298.1
mature peptide
806 .. 2719  =  1914 bp
Product: nsp2
produced by both pp1a and pp1ab
/protein_id=YP_009725298.1
mature peptide
2720 .. 8554  =  5835 bp
Product: nsp3
former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab
/protein_id=YP_009725299.1
mature peptide
2720 .. 8554  =  5835 bp
Product: nsp3
former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab
/protein_id=YP_009725299.1
mature peptide
8555 .. 10,054  =  1500 bp
Product: nsp4
nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab
/protein_id=YP_009725300.1
mature peptide
8555 .. 10,054  =  1500 bp
Product: nsp4
nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab
/protein_id=YP_009725300.1
mature peptide
10,055 .. 10,972  =  918 bp
Product: 3C-like proteinase
nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab
/protein_id=YP_009725301.1
mature peptide
10,055 .. 10,972  =  918 bp
Product: 3C-like proteinase
nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab
/protein_id=YP_009725301.1
mature peptide
10,973 .. 11,842  =  870 bp
Product: nsp6
nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab
/protein_id=YP_009725302.1
mature peptide
10,973 .. 11,842  =  870 bp
Product: nsp6
nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab
/protein_id=YP_009725302.1
mature peptide
11,843 .. 12,091  =  249 bp
Product: nsp7
produced by both pp1a and pp1ab
/protein_id=YP_009725303.1
mature peptide
11,843 .. 12,091  =  249 bp
Product: nsp7
produced by both pp1a and pp1ab
/protein_id=YP_009725303.1
mature peptide
12,092 .. 12,685  =  594 bp
Product: nsp8
produced by both pp1a and pp1ab
/protein_id=YP_009725304.1
mature peptide
12,092 .. 12,685  =  594 bp
Product: nsp8
produced by both pp1a and pp1ab
/protein_id=YP_009725304.1
mature peptide
12,686 .. 13,024  =  339 bp
Product: nsp9
ssRNA-binding protein; produced by both pp1a and pp1ab
/protein_id=YP_009725305.1
mature peptide
12,686 .. 13,024  =  339 bp
Product: nsp9
ssRNA-binding protein; produced by both pp1a and pp1ab
/protein_id=YP_009725305.1
mature peptide
13,025 .. 13,441  =  417 bp
Product: nsp10
nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab
/protein_id=YP_009725306.1
mature peptide
13,025 .. 13,441  =  417 bp
Product: nsp10
nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab
/protein_id=YP_009725306.1
mature peptide
13,442 .. 16,236  =  2795 bp
2 segments
   Segment 1:  
   13,442 .. 13,468  =  27 bp
Product: RNA-dependent RNA polymerase
nsp12; NiRAN and RdRp; produced by pp1ab only
/protein_id=YP_009725307.1
mature peptide
13,442 .. 16,236  =  2795 bp
2 segments
   Segment 2:  
   13,468 .. 16,236  =  2769 bp
Product: RNA-dependent RNA polymerase
nsp12; NiRAN and RdRp; produced by pp1ab only
/protein_id=YP_009725307.1
mature peptide
13,442 .. 16,236  =  2795 bp
2 segments
Product: RNA-dependent RNA polymerase
nsp12; NiRAN and RdRp; produced by pp1ab only
/protein_id=YP_009725307.1
stem loop
29,629 .. 29,657  =  29 bp
Function: Coronavirus 3' UTR pseudoknot stem-loop 2
stem loop
29,629 .. 29,657  =  29 bp
Function: Coronavirus 3' UTR pseudoknot stem-loop 2
mature peptide
13,442 .. 13,480  =  39 bp
Product: nsp11
produced by pp1a only
/protein_id=YP_009725312.1
mature peptide
13,442 .. 13,480  =  39 bp
Product: nsp11
produced by pp1a only
/protein_id=YP_009725312.1
stem loop
13,476 .. 13,503  =  28 bp
Function: Coronavirus frameshifting stimulation element stem-loop 1
stem loop
13,476 .. 13,503  =  28 bp
Function: Coronavirus frameshifting stimulation element stem-loop 1
ORF:  13,768 .. 21,555  =  7788 bp
ORF:  2595 amino acids  =  293.0 kDa
ORF:  25,393 .. 26,220  =  828 bp
ORF:  275 amino acids  =  31.1 kDa
ORF:  26,245 .. 26,472  =  228 bp
ORF:  75 amino acids  =  8.4 kDa
ORF:  27,394 .. 27,759  =  366 bp
ORF:  121 amino acids  =  13.7 kDa
ORF:  266 .. 13,483  =  13,218 bp
ORF:  4405 amino acids  =  490.0 kDa
ORF:  21,536 .. 25,384  =  3849 bp
ORF:  1282 amino acids  =  142.3 kDa
ORF:  28,274 .. 29,533  =  1260 bp
ORF:  419 amino acids  =  45.6 kDa
ORF:  2958 .. 3206  =  249 bp
ORF:  82 amino acids  =  9.6 kDa
ORF:  21,936 .. 22,199  =  264 bp
ORF:  87 amino acids  =  10.2 kDa
ORF:  26,523 .. 27,191  =  669 bp
ORF:  222 amino acids  =  25.1 kDa
ORF:  27,894 .. 28,259  =  366 bp
ORF:  121 amino acids  =  13.8 kDa
ORF:  28,284 .. 28,577  =  294 bp
ORF:  97 amino acids  =  10.8 kDa
ORF:  422 .. 667  =  246 bp
ORF:  81 amino acids  =  9.6 kDa
ORF:  23,198 .. 23,437  =  240 bp
ORF:  79 amino acids  =  9.1 kDa
ORF:  6187 .. 6489  =  303 bp
ORF:  100 amino acids  =  10.8 kDa
ORF:  23,074 .. 23,322  =  249 bp
ORF:  82 amino acids  =  8.9 kDa
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