LOCUS       sequence-399684-        6452 bp    DNA     circular SYN 15-APR-2025
DEFINITION  Overexpress HLA allele.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6452)
  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 6452)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Apr 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*55:02:01
FEATURES             Location/Qualifiers
     source          1..6452
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(13..30)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(184..772)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(264..283)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(943..1734,1735..1803))
                     /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     1566..1585
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(1804..1908)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(1983..2002)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        2174..2553
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        2554..2757
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     2708..2728
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     2802..2821
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        2802..2820
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(3982..3999)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    3988..4212
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      4258..4686
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(4345..4364)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     4555..4576
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(4695..4715)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        4700..5029
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      4880..5015
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     4942..4961
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             5096..5890
                     /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(5150..5169)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     5760..5779
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    6064..6185
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(6101..6120)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     6155..6174
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(6234..6250)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(6234..6250)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(6247..6269)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    6258..6274
                     /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(6282..6288,6289..6306,6307..6312))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    6327..6348
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
ORIGIN
        1 ctcttccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc ggcgagcggt
       61 atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata acgcaggaaa
      121 gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt aaaaaggccg cgttgctggc
      181 gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag
      241 gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa gctccctcgt
      301 gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc tcccttcggg
      361 aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt aggtcgttcg
      421 ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg ccttatccgg
      481 taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg cagcagccac
      541 tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct tgaagtggtg
      601 gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc tgaagccagt
      661 taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg ctggtagcgg
      721 tggttttttt gtttgcaagc agcagattac gcgcagaaaa aaaggatctc aagaagatcc
      781 tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt aagggatttt
      841 ggtcatgaga ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa aatgaagttt
      901 taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat gcttaatcag
      961 tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct gactccccgt
     1021 cgtgtagata actacgatac gggagggctt accatctggc cccagtgctg caatgatacc
     1081 gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag ccggaagggc
     1141 cgagcgcaga agtggtcctg caactttatc cgcctccatc cagtctatta attgttgccg
     1201 ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg ccattgctac
     1261 aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg gttcccaacg
     1321 atcaaggcga gttacatgat cccccatgtt gtgcaaaaaa gcggttagct ccttcggtcc
     1381 tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta tggcagcact
     1441 gcataattct cttactgtca tgccatccgt aagatgcttt tctgtgactg gtgagtactc
     1501 aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc cggcgtcaat
     1561 acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg gaaaacgttc
     1621 ttcggggcga aaactctcaa ggatcttacc gctgttgaga tccagttcga tgtaacccac
     1681 tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg ggtgagcaaa
     1741 aacaggaagg caaaatgccg caaaaaaggg aataagggcg acacggaaat gttgaatact
     1801 catactcttc ctttttcaat attattgaag catttatcag ggttattgtc tcatgagcgg
     1861 atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca catttccccg
     1921 aaaagtgcca cctgacgtcg acggatcggg agatctcccg atcccctatg gtgcactctc
     1981 agtacaatct gctctgatgc cgcatagtta agccagtatc tgctccctgc ttgtgtgttg
     2041 gaggtcgctg agtagtgcgc gagcaaaatt taagctacaa caaggcaagg cttgaccgac
     2101 aattgcatga agaatctgct tagggttagg cgttttgcgc tgcttcgcga tgtacgggcc
     2161 agatatacgc gttgacattg attattgact agttattaat agtaatcaat tacggggtca
     2221 ttagttcata gcccatatat ggagttccgc gttacataac ttacggtaaa tggcccgcct
     2281 ggctgaccgc ccaacgaccc ccgcccattg acgtcaataa tgacgtatgt tcccatagta
     2341 acgccaatag ggactttcca ttgacgtcaa tgggtggagt atttacggta aactgcccac
     2401 ttggcagtac atcaagtgta tcatatgcca agtacgcccc ctattgacgt caatgacggt
     2461 aaatggcccg cctggcatta tgcccagtac atgaccttat gggactttcc tacttggcag
     2521 tacatctacg tattagtcat cgctattacc atggtgatgc ggttttggca gtacatcaat
     2581 gggcgtggat agcggtttga ctcacgggga tttccaagtc tccaccccat tgacgtcaat
     2641 gggagtttgt tttggcacca aaatcaacgg gactttccaa aatgtcgtaa caactccgcc
     2701 ccattgacgc aaatgggcgg taggcgtgta cggtgggagg tctatataag cagagctctc
     2761 tggctaacta gagaacccac tgcttactgg cttatcgaaa ttaatacgac tcactatagg
     2821 gagacccaag ctggctagcg tttaaactta agcttgccac catgcgggtc acggcacccc
     2881 gaaccctcct cctgctgctc tggggggccc tggccctgac cgagacctgg gccggctccc
     2941 actccatgag gtatttctac accgccatgt cccggcccgg ccgcggggag ccccgcttca
     3001 tcgcagtggg ctacgtggac gacacgcagt tcgtgaggtt cgacagcgac gccgcgagtc
     3061 cgagagagga gccgcgggcg ccgtggatag agcaggaggg gccggagtat tgggaccgga
     3121 acacacagat ctacaaggcc caggcacaga ctgaccgaga gagcctgcgg aacctgcgcg
     3181 gctactacaa ccagagcgag gccgggtctc acacttggca gacgatgtat ggctgcgacc
     3241 tggggccgga cgggcgcctc ctccgcgggc ataaccagtt agcctacgac ggcaaggatt
     3301 acatcgccct gaacgaggac ctgagctcct ggaccgcggc ggacaccgcg gctcagatca
     3361 cccagcgcaa gtgggaggcg gcccgtgtgg cggagcagct gagagcctac ctggagggca
     3421 cgtgcgtgga gtggctccgc agatacctgg agaacgggaa ggagacgctg cagcgcgcgg
     3481 accccccaaa gacacacgtg acccaccacc ccatctctga ccatgaggcc accctgaggt
     3541 gctgggccct gggcttctac cctgcggaga tcacactgac ctggcagcgg gatggcgagg
     3601 accaaactca ggacactgag cttgtggaga ccagaccagc aggagataga accttccaga
     3661 agtgggcagc tgtggtggtg ccttctggag aagagcagag atacacatgc catgtacagc
     3721 atgaggggct gccgaagccc ctcaccctga gatgggagcc atcttcccag tccaccatcc
     3781 ccatcgtggg cattgttgct ggcctggctg tcctagcagt tgtggtcatc ggagctgtgg
     3841 tcgctactgt gatgtgtagg aggaagagct caggtggaaa aggagggagc tactctcagg
     3901 ctgcgtccag cgacagtgcc cagggctctg atgtgtctct cacagcttga tctagagggc
     3961 ccgtttaaac ccgctgatca gcctcgactg tgccttctag ttgccagcca tctgttgttt
     4021 gcccctcccc cgtgccttcc ttgaccctgg aaggtgccac tcccactgtc ctttcctaat
     4081 aaaatgagga aattgcatcg cattgtctga gtaggtgtca ttctattctg gggggtgggg
     4141 tggggcagga cagcaagggg gaggattggg aagacaatag caggcatgct ggggatgcgg
     4201 tgggctctat ggcttctgag gcggaaagaa ccagctgggg ctctaggggg tatccccacg
     4261 cgccctgtag cggcgcatta agcgcggcgg gtgtggtggt tacgcgcagc gtgaccgcta
     4321 cacttgccag cgccctagcg cccgctcctt tcgctttctt cccttccttt ctcgccacgt
     4381 tcgccggctt tccccgtcaa gctctaaatc gggggctccc tttagggttc cgatttagtg
     4441 ctttacggca cctcgacccc aaaaaacttg attagggtga tggttcacgt agtgggccat
     4501 cgccctgata gacggttttt cgccctttga cgttggagtc cacgttcttt aatagtggac
     4561 tcttgttcca aactggaaca acactcaacc ctatctcggt ctattctttt gatttataag
     4621 ggattttgcc gatttcggcc tattggttaa aaaatgagct gatttaacaa aaatttaacg
     4681 cgaattaatt ctgtggaatg tgtgtcagtt agggtgtgga aagtccccag gctccccagc
     4741 aggcagaagt atgcaaagca tgcatctcaa ttagtcagca accaggtgtg gaaagtcccc
     4801 aggctcccca gcaggcagaa gtatgcaaag catgcatctc aattagtcag caaccatagt
     4861 cccgccccta actccgccca tcccgcccct aactccgccc agttccgccc attctccgcc
     4921 ccatggctga ctaatttttt ttatttatgc agaggccgag gccgcctctg cctctgagct
     4981 attccagaag tagtgaggag gcttttttgg aggcctaggc ttttgcaaaa agctcccggg
     5041 agcttgtata tccattttcg gatctgatca agagacagga tgaggatcgt ttcgcatgat
     5101 tgaacaagat ggattgcacg caggttctcc ggccgcttgg gtggagaggc tattcggcta
     5161 tgactgggca caacagacaa tcggctgctc tgatgccgcc gtgttccggc tgtcagcgca
     5221 ggggcgcccg gttctttttg tcaagaccga cctgtccggt gccctgaatg aactgcagga
     5281 cgaggcagcg cggctatcgt ggctggccac gacgggcgtt ccttgcgcag ctgtgctcga
     5341 cgttgtcact gaagcgggaa gggactggct gctattgggc gaagtgccgg ggcaggatct
     5401 cctgtcatct caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg
     5461 gctgcatacg cttgatccgg ctacctgccc attcgaccac caagcgaaac atcgcatcga
     5521 gcgagcacgt actcggatgg aagccggtct tgtcgatcag gatgatctgg acgaagagca
     5581 tcaggggctc gcgccagccg aactgttcgc caggctcaag gcgcgcatgc ccgacggcga
     5641 ggatctcgtc gtgacccatg gcgatgcctg cttgccgaat atcatggtgg aaaatggccg
     5701 cttttctgga ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc
     5761 gttggctacc cgtgatattg ctgaagagct tggcggcgaa tgggctgacc gcttcctcgt
     5821 gctttacggt atcgccgctc ccgattcgca gcgcatcgcc ttctatcgcc ttcttgacga
     5881 gttcttctga gcgggactct ggggttcgaa atgaccgacc aagcgacgcc caacctgcca
     5941 tcacgagatt tcgattccac cgccgccttc tatgaaaggt tgggcttcgg aatcgttttc
     6001 cgggacgccg gctggatgat cctccagcgc ggggatctca tgctggagtt cttcgcccac
     6061 cccaacttgt ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc
     6121 acaaataaag catttttttc actgcattct agttgtggtt tgtccaaact catcaatgta
     6181 tcttatcatg tctgtatacc gtcgacctct agctagagct tggcgtaatc atggtcatag
     6241 ctgtttcctg tgtgaaattg ttatccgctc acaattccac acaacatacg agccggaagc
     6301 ataaagtgta aagcctgggg tgcctaatga gtgagctaac tcacattaat tgcgttgcgc
     6361 tcactgcccg ctttccagtc gggaaacctg tcgtgccagc tgcattaatg aatcggccaa
     6421 cgcgcgggga gaggcggttt gcgtattggg cg
//
