LOCUS       sequence-399900-        6503 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Overexpress HLA allele.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6503)
  AUTHORS   Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, 
            Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, 
            Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, 
            Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen 
            N, Carr SA, Wu CJ, Keskin DB
  TITLE     A large peptidome dataset improves HLA class I epitope prediction 
            across most of the human population.
  JOURNAL   Nat Biotechnol. 2020 Feb;38(2):199-209. doi: 
            10.1038/s41587-019-0322-9. Epub 2019 Dec 16.
  PUBMED    31844290
REFERENCE   2  (bases 1 to 6503)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; doi: 
            "10.1038/s41587-019-0322-9"; journalName: "Nat Biotechnol"; date: 
            "2020-02"; volume: "38"; issue: "2"; pages: "199-209"
COMMENT     Sequence Label: B*40:01:01
FEATURES             Location/Qualifiers
     source          1..6503
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(44..63)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        235..614
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        615..818
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     769..789
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     863..882
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        863..881
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(2094..2111)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2100..2324
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2370..2798
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2457..2476)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2667..2688
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2807..2827)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2812..3141
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2992..3127
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3054..3073
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3208..4002
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(3262..3281)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3872..3891
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4176..4297
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4213..4232)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4267..4286
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4346..4362)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4346..4362)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4359..4381)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4370..4386
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(4394..4400,4401..4418,4419..4424))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4439..4460
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4577..4594)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4748..5336)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4828..4847)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5507..6298,6299..6367))
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     6130..6149
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6368..6472)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 gacggatcgg gagatctccc gatcccctat ggtgcactct cagtacaatc tgctctgatg
       61 ccgcatagtt aagccagtat ctgctccctg cttgtgtgtt ggaggtcgct gagtagtgcg
      121 cgagcaaaat ttaagctaca acaaggcaag gcttgaccga caattgcatg aagaatctgc
      181 ttagggttag gcgttttgcg ctgcttcgcg atgtacgggc cagatatacg cgttgacatt
      241 gattattgac tagttattaa tagtaatcaa ttacggggtc attagttcat agcccatata
      301 tggagttccg cgttacataa cttacggtaa atggcccgcc tggctgaccg cccaacgacc
      361 cccgcccatt gacgtcaata atgacgtatg ttcccatagt aacgccaata gggactttcc
      421 attgacgtca atgggtggag tatttacggt aaactgccca cttggcagta catcaagtgt
      481 atcatatgcc aagtacgccc cctattgacg tcaatgacgg taaatggccc gcctggcatt
      541 atgcccagta catgacctta tgggactttc ctacttggca gtacatctac gtattagtca
      601 tcgctattac catggtgatg cggttttggc agtacatcaa tgggcgtgga tagcggtttg
      661 actcacgggg atttccaagt ctccacccca ttgacgtcaa tgggagtttg ttttggcacc
      721 aaaatcaacg ggactttcca aaatgtcgta acaactccgc cccattgacg caaatgggcg
      781 gtaggcgtgt acggtgggag gtctatataa gcagagctct ctggctaact agagaaccca
      841 ctgcttactg gcttatcgaa attaatacga ctcactatag ggagacccaa gctggctagc
      901 gtttaaactt aagcttggta ccgagctcgg atccatgcgg gtcacggcac cccgaaccgt
      961 cctcctgctg ctctcggcgg ccctggccct gaccgagacc tgggcgggct cccactccat
     1021 gaggtatttc cacaccgcca tgtcccggcc cggccgcggg gagccccgct tcatcaccgt
     1081 gggctacgtg gacgacacgc tgttcgtgag gttcgacagc gacgccacga gtccgaggaa
     1141 ggagccgcgg gcgccatgga tagagcagga ggggccggag tattgggacc gggagacaca
     1201 gatctccaag accaacacac agacttaccg agagagcctg cggaacctgc gcggctacta
     1261 caaccagagc gaggccgggt ctcacaccct ccagaggatg tacggctgcg acgtggggcc
     1321 ggacgggcgc ctcctccgcg ggcataacca gtacgcctac gacggcaagg attacatcgc
     1381 cctgaacgag gacctgcgct cctggaccgc cgcggacacg gcggctcaga tctcccagcg
     1441 caagttggag gcggcccgtg tggcggagca gctgagagcc tacctggagg gcgagtgcgt
     1501 ggagtggctc cgcagatacc tggagaacgg gaaggacaag ctggagcgcg ctgacccccc
     1561 aaagacacac gtgacccacc accccatctc tgaccatgag gccaccctga ggtgctgggc
     1621 cctgggtttc taccctgcgg agatcacact gacctggcag cgggatggcg aggaccaaac
     1681 tcaggacact gagcttgtgg agaccagacc agcaggagat agaaccttcc agaagtgggc
     1741 agctgtggtg gtgccttctg gagaagagca gagatacaca tgccatgtac agcatgaggg
     1801 gctgccgaag cccctcaccc tgagatggga gccgtcttcc cagtccaccg tccccatcgt
     1861 gggcattgtt gctggcctgg ctgtcctagc agttgtggtc atcggagctg tggtcgctgc
     1921 tgtgatgtgt aggaggaaga gttcaggtgg aaaaggaggg agctactctc aggctgcgtg
     1981 cagcgacagt gcccagggct ctgatgtgtc tctcacagct tgagaattct gcagatatcc
     2041 agcacagtgg cggccgctcg agtctagagg gcccgtttaa acccgctgat cagcctcgac
     2101 tgtgccttct agttgccagc catctgttgt ttgcccctcc cccgtgcctt ccttgaccct
     2161 ggaaggtgcc actcccactg tcctttccta ataaaatgag gaaattgcat cgcattgtct
     2221 gagtaggtgt cattctattc tggggggtgg ggtggggcag gacagcaagg gggaggattg
     2281 ggaagacaat agcaggcatg ctggggatgc ggtgggctct atggcttctg aggcggaaag
     2341 aaccagctgg ggctctaggg ggtatcccca cgcgccctgt agcggcgcat taagcgcggc
     2401 gggtgtggtg gttacgcgca gcgtgaccgc tacacttgcc agcgccctag cgcccgctcc
     2461 tttcgctttc ttcccttcct ttctcgccac gttcgccggc tttccccgtc aagctctaaa
     2521 tcgggggctc cctttagggt tccgatttag tgctttacgg cacctcgacc ccaaaaaact
     2581 tgattagggt gatggttcac gtagtgggcc atcgccctga tagacggttt ttcgcccttt
     2641 gacgttggag tccacgttct ttaatagtgg actcttgttc caaactggaa caacactcaa
     2701 ccctatctcg gtctattctt ttgatttata agggattttg ccgatttcgg cctattggtt
     2761 aaaaaatgag ctgatttaac aaaaatttaa cgcgaattaa ttctgtggaa tgtgtgtcag
     2821 ttagggtgtg gaaagtcccc aggctcccca gcaggcagaa gtatgcaaag catgcatctc
     2881 aattagtcag caaccaggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa
     2941 agcatgcatc tcaattagtc agcaaccata gtcccgcccc taactccgcc catcccgccc
     3001 ctaactccgc ccagttccgc ccattctccg ccccatggct gactaatttt ttttatttat
     3061 gcagaggccg aggccgcctc tgcctctgag ctattccaga agtagtgagg aggctttttt
     3121 ggaggcctag gcttttgcaa aaagctcccg ggagcttgta tatccatttt cggatctgat
     3181 caagagacag gatgaggatc gtttcgcatg attgaacaag atggattgca cgcaggttct
     3241 ccggccgctt gggtggagag gctattcggc tatgactggg cacaacagac aatcggctgc
     3301 tctgatgccg ccgtgttccg gctgtcagcg caggggcgcc cggttctttt tgtcaagacc
     3361 gacctgtccg gtgccctgaa tgaactgcag gacgaggcag cgcggctatc gtggctggcc
     3421 acgacgggcg ttccttgcgc agctgtgctc gacgttgtca ctgaagcggg aagggactgg
     3481 ctgctattgg gcgaagtgcc ggggcaggat ctcctgtcat ctcaccttgc tcctgccgag
     3541 aaagtatcca tcatggctga tgcaatgcgg cggctgcata cgcttgatcc ggctacctgc
     3601 ccattcgacc accaagcgaa acatcgcatc gagcgagcac gtactcggat ggaagccggt
     3661 cttgtcgatc aggatgatct ggacgaagag catcaggggc tcgcgccagc cgaactgttc
     3721 gccaggctca aggcgcgcat gcccgacggc gaggatctcg tcgtgaccca tggcgatgcc
     3781 tgcttgccga atatcatggt ggaaaatggc cgcttttctg gattcatcga ctgtggccgg
     3841 ctgggtgtgg cggaccgcta tcaggacata gcgttggcta cccgtgatat tgctgaagag
     3901 cttggcggcg aatgggctga ccgcttcctc gtgctttacg gtatcgccgc tcccgattcg
     3961 cagcgcatcg ccttctatcg ccttcttgac gagttcttct gagcgggact ctggggttcg
     4021 aaatgaccga ccaagcgacg cccaacctgc catcacgaga tttcgattcc accgccgcct
     4081 tctatgaaag gttgggcttc ggaatcgttt tccgggacgc cggctggatg atcctccagc
     4141 gcggggatct catgctggag ttcttcgccc accccaactt gtttattgca gcttataatg
     4201 gttacaaata aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt
     4261 ctagttgtgg tttgtccaaa ctcatcaatg tatcttatca tgtctgtata ccgtcgacct
     4321 ctagctagag cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc
     4381 tcacaattcc acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat
     4441 gagtgagcta actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc
     4501 tgtcgtgcca gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg
     4561 ggcgctcttc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag
     4621 cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag
     4681 gaaagaacat gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc
     4741 tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc
     4801 agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc
     4861 tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc tttctccctt
     4921 cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg
     4981 ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
     5041 ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca ctggcagcag
     5101 ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt
     5161 ggtggcctaa ctacggctac actagaagaa cagtatttgg tatctgcgct ctgctgaagc
     5221 cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta
     5281 gcggtggttt ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag
     5341 atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca cgttaaggga
     5401 ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa
     5461 gttttaaatc aatctaaagt atatatgagt aaacttggtc tgacagttac caatgcttaa
     5521 tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc
     5581 ccgtcgtgta gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga
     5641 taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag ccagccggaa
     5701 gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt
     5761 gccgggaagc tagagtaagt agttcgccag ttaatagttt gcgcaacgtt gttgccattg
     5821 ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc
     5881 aacgatcaag gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg
     5941 gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg gttatggcag
     6001 cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt
     6061 actcaaccaa gtcattctga gaatagtgta tgcggcgacc gagttgctct tgcccggcgt
     6121 caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac
     6181 gttcttcggg gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac
     6241 ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt tctgggtgag
     6301 caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa
     6361 tactcatact cttccttttt caatattatt gaagcattta tcagggttat tgtctcatga
     6421 gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc
     6481 cccgaaaagt gccacctgac gtc
//
