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2957_HDM_Spikedelta21_B.1.351.gb
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2957_HDM_Spikedelta21_B.1.351.gb
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LOCUS Exported 8305 bp ds-DNA circular SYN 07-JAN-2021
DEFINITION Jesse Bloom created this plasmid. It is an HDM plasmid where inserts
can be cloned into a 5' NotI site and a 3' BamHI site. I created
this plasmid by cutting the VSVG out of HDM-VSVG with EcoRI.
CHARACTERIZATION: * Confirmed by sequencing region from nt 1234 -
2068 (1-22-08) Kate cloned IDT codon optimized SARS-CoV-2 Spike into
plasmid 44 after digesting with EcoRI and HindIII. Kate inserted a
'cgccacc' 5' to the gene start site (following the EcoRI restriction
site to have a good 5' Kozak sequence). Insert confirmed via Sanger
Sequencing in April 2020 by Rachel Eguia. This resulted in plasmid
2736. Additional cloning was conducted to delete a 21 amino acid
region from the C-terminal end of the Spike protein. Spike deletion
confirmed by Sanger Sequencing in May 2020 by Rachel. The following
mutations were added by Andrea Loes to derive a representative Spike
sequence of the B.7.351 lineage, circulating in South Africa in
early 2021 (also known as the 501Y.V2 lineage) - D80A, D215G,
L242-244del, K417N, E484K, N501Y, A701V. The amino acid sequence is consistent with EPI_ISL_700420.
ACCESSION .
VERSION .
KEYWORDS .
SOURCE synthetic DNA construct
ORGANISM synthetic DNA construct
REFERENCE 1 (bases 1 to 8305)
AUTHORS .
TITLE Direct Submission
JOURNAL Exported Jan 7, 2021 from SnapGene Viewer 4.2.11
http://www.snapgene.com
FEATURES Location/Qualifiers
source 1..8305
/organism="synthetic DNA construct"
/mol_type="other DNA"
misc_feature 1..7
/label=kozak
misc_feature 8..3760
/label=nCoV_IDT_opt_spike
misc_feature 245..247
/label=D80A
misc_feature 650..652
/label=D215G
misc_feature 728..730
/label=L242-244del
misc_feature 1247..1249
/label=K417N
misc_feature 1448..1450
/label=E484K
misc_feature 1499..1501
/label=N501Y
misc_feature 1838..1840
/label=D614G
misc_feature 2099..2101
/label=A701V
misc_feature 3761..3766
/label=HindIII
misc_feature 3799..4558
/label=beta_globin_pA
primer_bind complement(3845..3862)
/label=primer_bind
primer_bind 3968..3996
/label=primer_bind
polyA_site 3986..4010
/label=polyA_site
primer_bind complement(4053..4077)
/label=primer_bind
primer_bind 4269..4302
/label=primer_bind
primer_bind complement(4348..4378)
/label=primer_bind
misc_feature 4534..4558
/label=End_of_globin
misc_feature 4572..4609
/label=Correction-143
primer_bind complement(4611..4641)
/label=primer_bind
CDS 4798..5655
/label=bla
primer_bind 4832..4852
/label=primer_bind
primer_bind complement(4918..4941)
/label=primer_bind
primer_bind 5132..5159
/label=primer_bind
primer_bind complement(5221..5241)
/label=primer_bind
primer_bind 5432..5456
/label=primer_bind
primer_bind complement(5520..5541)
/label=primer_bind
primer_bind 5732..5760
/label=primer_bind
primer_bind complement(5812..5841)
/label=primer_bind
misc_feature 5954..5997
/label=High_copy
primer_bind 6032..6059
/label=primer_bind
primer_bind complement(6123..6141)
/label=primer_bind
primer_bind 6332..6357
/label=primer_bind
misc_feature 6418..6443
/label=Correction-133
misc_feature 6685..6712
/label=Correction-134
primer_bind 6838..6863
/label=primer_bind
misc_feature 6885..6997
/label=SV40_ori
primer_bind complement(6910..6936)
/label=primer_bind
promoter 7006..7676
/label=CMV
promoter 7093..7676
/label=CMV
primer_bind 7148..7175
/label=primer_bind
primer_bind complement(7233..7257)
/label=primer_bind
primer_bind complement(7533..7557)
/label=primer_bind
primer_bind 7558..7590
/label=primer_bind
primer_bind 7609..7649
/label=primer_bind
primer_bind 7614..7635
/label=primer_bind
misc_feature 7625..7676
/label=CMV_TATA
primer_bind complement(7659..7700)
/label=primer_bind
misc_feature 7677..7747
/label=CMV_5xxUTR
primer_bind 7689..7712
/label=primer_bind
primer_bind 7748..7772
/label=primer_bind
misc_feature 7776..8251
/label=B-globin_intron
primer_bind complement(7830..7857)
/label=primer_bind
primer_bind complement(7949..7978)
/label=primer_bind
primer_bind 8048..8079
/label=primer_bind
primer_bind complement(8132..8157)
/label=primer_bind
primer_bind 8206..8240
/label=primer_bind
primer_bind 8221..8241
/label=primer_bind
primer_bind 8223..8250
/label=primer_bind
primer_bind join(8281..8305,1..13)
/label=cloningmutprimer_F
misc_feature 8300..8305
/label=EcoRI
ORIGIN
1 cgccaccatg ttcgtgttcc tggtactcct tcctttggtg tcttcccagt gtgtaaatct
61 taccactcgg acccagcttc cacccgccta caccaacagt ttcacacgcg gcgtctacta
121 tcctgacaag gtgtttagga gttcagtctt gcactcaact caagacttgt tcctcccttt
181 ctttagcaat gtgacgtggt ttcatgccat tcatgtctcc ggcacaaacg gaacgaagcg
241 ctttgctaat cctgtgctcc cgttcaacga tggagtgtac ttcgcgtcca cagagaagag
301 caatatcatt cgaggttgga tcttcggaac gacactcgac tcaaagacgc agtcccttct
361 catcgtcaat aatgccacga acgtggtcat caaagtgtgc gagtttcaat tctgtaatga
421 tcccttcctg ggcgtctatt atcacaagaa caacaaatcc tggatggagt ccgaatttag
481 agtctactcc agcgccaaca actgcacttt cgaatacgta tcacagccat tcttgatgga
541 ccttgaagga aagcagggta atttcaagaa cttgagggag ttcgtattca agaatatcga
601 cgggtacttt aagatttata gcaaacacac acccattaat ttggtgcggg gacttcctca
661 gggatttagt gctcttgagc ctctcgttga cctccctatt ggcattaaca tcacccgctt
721 tcaaaccctg catcggtcct acctgacacc gggcgactca agttccggat ggaccgcagg
781 tgccgccgca tactatgtgg gctaccttca gccaagaaca tttctgctga aatataatga
841 gaacgggacc attacagatg cggtggattg tgcactcgac cctctgtctg agacgaaatg
901 cacccttaag agcttcacgg tggagaaagg catttatcag acttctaact tcagagttca
961 acccaccgag tccattgtgc gattcccaaa tattacgaat ttgtgcccat ttggtgaggt
1021 cttcaatgct actcgattcg cctcagttta tgcatggaac cgaaagagaa tttccaattg
1081 tgtggcggac tactcagtat tgtataatag tgcaagcttt agcacattca aatgttacgg
1141 cgtgtctcca acgaagctga acgatctctg tttcacaaac gtttatgcgg attccttcgt
1201 gattcgcggc gatgaggtcc gacagattgc gcctgggcaa acgggtaaca tcgctgatta
1261 caactataag ttgccggacg atttcacagg atgtgtcata gcttggaata gcaataattt
1321 ggacagtaag gttggcggaa actacaatta tttgtacagg ttgtttcgca agtcaaattt
1381 gaaaccattt gagagagata tatctacgga gatatatcaa gccggctcta caccatgtaa
1441 tggtgtgaag ggctttaact gctactttcc actccagtca tatggtttcc aacctacata
1501 tggagtaggg tatcaaccgt acagagttgt ggtcttgagt ttcgaattgc tccacgctcc
1561 agcaacggta tgcggtccta agaaatccac aaatcttgtg aagaacaagt gcgtaaattt
1621 caacttcaat gggctgactg gaacaggcgt gctgactgag agtaacaaga agttcttgcc
1681 tttccaacaa ttcgggcggg acatagctga taccactgac gccgtccgcg accctcagac
1741 cctggagatt ctggacataa ctccttgttc tttcggtggc gtcagtgtta tcactcccgg
1801 gaccaacacc tccaaccaag tcgcggtcct ctatcaaggc gtcaactgta cggaagtacc
1861 ggtagccatc catgcggacc aacttacacc gacttggagg gtttactcta caggaagcaa
1921 tgtctttcaa acacgagccg ggtgtctgat cggagcagaa cacgttaaca acagctacga
1981 atgtgacata ccaataggcg cagggatttg tgcttcatat cagacacaga ccaatagccc
2041 gcggagagcg agaagcgtag caagccaaag catcatcgcg tacacgatga gcctcggagt
2101 ggagaacagc gtcgcgtata gcaataattc aatagctatc ccaacaaatt tcactatttc
2161 ggtcaccact gagattctgc cggtctccat gaccaagaca tccgtcgatt gtactatgta
2221 catatgcggc gacagcacgg agtgcagtaa cttgctcctt cagtacggtt ccttctgtac
2281 gcagcttaac cgggcactga cgggtatcgc ggtagaacag gacaagaaca cacaggaggt
2341 cttcgcgcag gtcaaacaaa tctacaagac accacccata aaggacttcg gcgggttcaa
2401 tttcagccaa atcctgccgg acccttccaa acctagtaag aggtcattca ttgaggatct
2461 tctgtttaac aaagttacgc ttgcggacgc gggattcatt aagcagtatg gtgactgcct
2521 tggagatatt gccgccaggg atttgatatg tgcacagaaa tttaacggcc tcaccgttct
2581 gccgcctctg ctcaccgatg agatgatagc gcagtacacg agcgcactcc tggcaggtac
2641 aattacaagc ggatggacat tcggtgcagg agcagcgttg cagataccct ttgctatgca
2701 gatggcttat cgatttaacg ggattggcgt cacgcagaac gtcctttatg agaatcagaa
2761 attgattgca aatcagttca atagtgctat cggtaagatt caggacagct tgagcagtac
2821 cgcgtctgca ctgggaaagt tgcaggacgt ggtgaatcag aatgcacaag cactgaatac
2881 cttggttaag caattgagta gcaatttcgg cgccatatca agtgtactga atgatatcct
2941 gtcacggttg gacaaggtag aagccgaagt tcagattgac cgcttgatca ccgggcgcct
3001 ccaaagtctg cagacctacg tcacacaaca attgatcaga gcagcagaga taagagcatc
3061 tgctaacctg gctgccacta agatgtctga atgtgtgctt gggcagtcaa agagggtaga
3121 tttctgcgga aagggctacc accttatgtc tttccctcag agcgctccgc atggtgtggt
3181 ctttctccat gtgacttatg tgcctgctca agagaagaac tttacgacgg cgcccgctat
3241 atgccatgat ggtaaggcgc actttccaag ggagggagtg ttcgtgtcca acggcactca
3301 ctggtttgtc acccaacgaa atttctacga gcctcaaatt attaccaccg acaatacctt
3361 tgttagcggt aactgtgacg tcgtaattgg gattgttaat aatacagtct acgatcctct
3421 gcagccggaa ctggactcct ttaaagagga gctggacaaa tatttcaaga accacacatc
3481 tcctgacgta gatcttggag acataagcgg tataaatgca agtgttgtta acattcagaa
3541 agaaatagat aggttgaacg aagttgcgaa gaaccttaac gagtcactga tagacctcca
3601 agagcttggg aagtacgagc aatatatcaa gtggccttgg tatatttggc tcgggttcat
3661 agcaggactt atcgctatag tcatggtgac tataatgctg tgctgcatga caagctgctg
3721 cagctgtctc aaaggctgtt gctcttgcgg ctcttaatga aagcttatcg ataccgtcga
3781 cctcgagggc ccagatctaa ttcaccccac cagtgcaggc tgcctatcag aaagtggtgg
3841 ctggtgtggc taatgccctg gcccacaagt atcactaagc tcgctttctt gctgtccaat
3901 ttctattaaa ggttcctttg ttccctaagt ccaactacta aactggggga tattatgaag
3961 ggccttgagc atctggattc tgcctaataa aaaacattta ttttcattgc aatgatgtat
4021 ttaaattatt tctgaatatt ttactaaaaa gggaatgtgg gaggtcagtg catttaaaac
4081 ataaagaaat gaagagctag ttcaaacctt gggaaaatac actatatctt aaactccatg
4141 aaagaaggtg aggctgcaaa cagctaatgc acattggcaa cagcccctga tgcctatgcc
4201 ttattcatcc ctcagaaaag gattcaagta gaggcttgat ttggaggtta aagttttgct
4261 atgctgtatt ttacattact tattgtttta gctgtcctca tgaatgtctt ttcactaccc
4321 atttgcttat cctgcatctc tcagccttga ctccactcag ttctcttgct tagagatacc
4381 acctttcccc tgaagtgttc cttccatgtt ttacggcgag atggtttctc ctcgcctggc
4441 cactcagcct tagttgtctc tgttgtctta tagaggtcta cttgaagaag gaaaaacagg
4501 gggcatggtt tgactgtcct gtgagccctt cttccctgcc tcccccactc acagtgaccc
4561 ggaatccctc gacatggcag tctagatcat tcttgaagac gaaagggcct cgtgatacgc
4621 ctatttttat aggttaatgt catgataata atggtttctt agacgtcagg tggcactttt
4681 cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat
4741 ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag gaagagtatg
4801 agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt
4861 tttgctcacc cagaaacgct ggtgaaagta aaagatgctg aagatcagtt gggtgcacga
4921 gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa
4981 gaacgttttc caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt
5041 attgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa tgacttggtt
5101 gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc
5161 agtgctgcca taaccatgag tgataacact gcggccaact tacttctgac aacgatcgga
5221 ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat
5281 cgttgggaac cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct
5341 gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac tctagcttcc
5401 cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg
5461 gcccttccgg ctggctggtt tattgctgat aaatctggag ccggtgagcg tgggtctcgc
5521 ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg
5581 acggggagtc aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca
5641 ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta gattgattta
5701 aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc
5761 aaaatccctt aacgtgagtt ttcgttccac tgagcgtcag accccgtaga aaagatcaaa
5821 ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca
5881 ccgctaccag cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta
5941 actggcttca gcagagcgca gataccaaat actgttcttc tagtgtagcc gtagttaggc
6001 caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca
6061 gtggctgctg ccagtggcga taagtcgtgt cttaccgggt tggactcaag acgatagtta
6121 ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag
6181 cgaacgacct acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt
6241 cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac aggagagcgc
6301 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
6361 ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
6421 gccagcaacg gatgcgccgc gtgcggctgc tggagatggc ggacgcgatg gatatgttct
6481 gccaagggtt ggtttgcgca ttcacagttc tccgcaagaa ttgattggct ccaattcttg
6541 gagtggtgaa tccgttagcg aggtgccgcc ggcttccatt caggtcgagg tggcccggct
6601 ccatgcaccg cgacgcaacg cggggaggca gacaaggtat agggcggcgc ctacaatcca
6661 tgccaacccg ttccatgtgc tcgccgaggc ggcataaatc cccgtgacga tcagcggtcc
6721 aatgatcgaa gttaggctgg taagagccgc gagcgatcct tgaagctgtc cctgatggtc
6781 gtcatctacc tgcctggaca gcatggcctg caacgcgggc atcccgatgc cgccggaagc
6841 gagaagaatc ataatgggga aggccatcca gcctcgcgtc ggggagcttt ttgcaaaagc
6901 ctaggcctcc aaaaaagcct cctcactact tctggaatag ctcagaggcc gaggcggcct
6961 cggcctctgc ataaataaaa aaaattagtc agccatgagc ttggcccatt gcatacgttg
7021 tatccatatc ataatatgta catttatatt ggctcatgtc caacattacc gccatgttga
7081 cattgattat tgactagtta ttaatagtaa tcaattacgg ggtcattagt tcatagccca
7141 tatatggagt tccgcgttac ataacttacg gtaaatggcc cgcctggctg accgcccaac
7201 gacccccgcc cattgacgtc aataatgacg tatgttccca tagtaacgcc aatagggact
7261 ttccattgac gtcaatgggt ggagtattta cggtaaactg cccacttggc agtacatcaa
7321 gtgtatcata tgccaagtac gccccctatt gacgtcaatg acggtaaatg gcccgcctgg
7381 cattatgccc agtacatgac cttatgggac tttcctactt ggcagtacat ctacgtatta
7441 gtcatcgcta ttaccatggt gatgcggttt tggcagtaca tcaatgggcg tggatagcgg
7501 tttgactcac ggggatttcc aagtctccac cccattgacg tcaatgggag tttgttttgg
7561 caccaaaatc aacgggactt tccaaaatgt cgtaacaact ccgccccatt gacgcaaatg
7621 ggcggtaggc gtgtacggtg ggaggtctat ataagcagag ctcgtttagt gaaccgtcag
7681 atcgcctgga gacgccatcc acgctgtttt gacctccata gaagacaccg ggaccgatcc
7741 agcctcccct cgaagctgat cctgagaact tcagggtgag tctatgggac ccttgatgtt
7801 ttctttcccc ttcttttcta tggttaagtt catgtcatag gaaggggaga agtaacaggg
7861 tacacatatt gaccaaatca gggtaatttt gcatttgtaa ttttaaaaaa tgctttcttc
7921 ttttaatata cttttttgtt tatcttattt ctaatacttt ccctaatctc tttctttcag
7981 ggcaataatg atacaatgta tcatgcctct ttgcaccatt ctaaagaata acagtgataa
8041 tttctgggtt aaggcaatag caatatttct gcatataaat atttctgcat ataaattgta
8101 actgatgtaa gaggtttcat attgctaata gcagctacaa tccagctacc attctgcttt
8161 tattttatgg ttgggataag gctggattat tctgagtcca agctaggccc ttttgctaat
8221 catgttcata cctcttatct tcctcccaca gctcctgggc aacgtgctgg tctgtgtgct
8281 ggcccatcac tttggcaaag aattc
//