LOCUS       sequence-399863-        6518 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 6518)
  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 6518)
  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: A*24:02:01
FEATURES             Location/Qualifiers
     source          1..6518
                     /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"
     regulatory      935..944
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     primer_bind     complement(2109..2126)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2115..2339
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2385..2813
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2472..2491)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2682..2703
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2822..2842)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2827..3156
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      3007..3142
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3069..3088
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3223..4017
                     /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(3277..3296)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3887..3906
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4191..4312
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4228..4247)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4282..4301
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4361..4377)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4361..4377)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4374..4396)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4385..4401
                     /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(4409..4415,4416..4433,4434..4439))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4454..4475
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4592..4609)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4763..5351)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4843..4862)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5522..6313,6314..6382))
                     /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     6145..6164
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6383..6487)
                     /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 atccgccacc atggccgtca tggcgccccg
      961 aaccctcgtc ctgctactct cgggggccct ggccctgacc cagacctggg caggctccca
     1021 ctccatgagg tatttctcca catccgtgtc ccggcccggc cgcggggagc cccgcttcat
     1081 cgccgtgggc tacgtggacg acacgcagtt cgtgcggttc gacagcgacg ccgcgagcca
     1141 gaggatggag ccgcgggcgc cgtggataga gcaggagggg ccggagtatt gggacgagga
     1201 gacagggaaa gtgaaggccc actcacagac tgaccgagag aacctgcgga tcgcgctccg
     1261 ctactacaac cagagcgagg ccggttctca caccctccag atgatgtttg gctgcgacgt
     1321 ggggtcggac gggcgcttcc tccgcgggta ccaccagtac gcctacgacg gcaaggatta
     1381 catcgccctg aaagaggacc tgcgctcttg gaccgcggcg gacatggcgg ctcagatcac
     1441 caagcgcaag tgggaggcgg cccatgtggc ggagcagcag agagcctacc tggagggcac
     1501 gtgcgtggac gggctccgca gatacctgga gaacgggaag gagacgctgc agcgcacgga
     1561 cccccccaag acacatatga cccaccaccc catctctgac catgaggcca ctctgagatg
     1621 ctgggccctg ggcttctacc ctgcggagat cacactgacc tggcagcggg atggggagga
     1681 ccagacccag gacacggagc ttgtggagac caggcctgca ggggatggaa ccttccagaa
     1741 gtgggcagct gtggtggtac cttctggaga ggagcagaga tacacctgcc atgtgcagca
     1801 tgagggtctg cccaagcccc tcaccctgag atgggagcca tcttcccagc ccaccgtccc
     1861 catcgtgggc atcattgctg gcctggttct ccttggagct gtgatcactg gagctgtggt
     1921 cgctgctgtg atgtggagga ggaacagctc agatagaaaa ggagggagct actctcaggc
     1981 tgcaagcagt gacagtgccc agggctctga tgtgtctctc acagcttgta aagtgtgaga
     2041 attctgcaga tatccagcac agtggcggcc gctcgagtct agagggcccg tttaaacccg
     2101 ctgatcagcc tcgactgtgc cttctagttg ccagccatct gttgtttgcc cctcccccgt
     2161 gccttccttg accctggaag gtgccactcc cactgtcctt tcctaataaa atgaggaaat
     2221 tgcatcgcat tgtctgagta ggtgtcattc tattctgggg ggtggggtgg ggcaggacag
     2281 caagggggag gattgggaag acaatagcag gcatgctggg gatgcggtgg gctctatggc
     2341 ttctgaggcg gaaagaacca gctggggctc tagggggtat ccccacgcgc cctgtagcgg
     2401 cgcattaagc gcggcgggtg tggtggttac gcgcagcgtg accgctacac ttgccagcgc
     2461 cctagcgccc gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc
     2521 ccgtcaagct ctaaatcggg ggctcccttt agggttccga tttagtgctt tacggcacct
     2581 cgaccccaaa aaacttgatt agggtgatgg ttcacgtagt gggccatcgc cctgatagac
     2641 ggtttttcgc cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac
     2701 tggaacaaca ctcaacccta tctcggtcta ttcttttgat ttataaggga ttttgccgat
     2761 ttcggcctat tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attaattctg
     2821 tggaatgtgt gtcagttagg gtgtggaaag tccccaggct ccccagcagg cagaagtatg
     2881 caaagcatgc atctcaatta gtcagcaacc aggtgtggaa agtccccagg ctccccagca
     2941 ggcagaagta tgcaaagcat gcatctcaat tagtcagcaa ccatagtccc gcccctaact
     3001 ccgcccatcc cgcccctaac tccgcccagt tccgcccatt ctccgcccca tggctgacta
     3061 atttttttta tttatgcaga ggccgaggcc gcctctgcct ctgagctatt ccagaagtag
     3121 tgaggaggct tttttggagg cctaggcttt tgcaaaaagc tcccgggagc ttgtatatcc
     3181 attttcggat ctgatcaaga gacaggatga ggatcgtttc gcatgattga acaagatgga
     3241 ttgcacgcag gttctccggc cgcttgggtg gagaggctat tcggctatga ctgggcacaa
     3301 cagacaatcg gctgctctga tgccgccgtg ttccggctgt cagcgcaggg gcgcccggtt
     3361 ctttttgtca agaccgacct gtccggtgcc ctgaatgaac tgcaggacga ggcagcgcgg
     3421 ctatcgtggc tggccacgac gggcgttcct tgcgcagctg tgctcgacgt tgtcactgaa
     3481 gcgggaaggg actggctgct attgggcgaa gtgccggggc aggatctcct gtcatctcac
     3541 cttgctcctg ccgagaaagt atccatcatg gctgatgcaa tgcggcggct gcatacgctt
     3601 gatccggcta cctgcccatt cgaccaccaa gcgaaacatc gcatcgagcg agcacgtact
     3661 cggatggaag ccggtcttgt cgatcaggat gatctggacg aagagcatca ggggctcgcg
     3721 ccagccgaac tgttcgccag gctcaaggcg cgcatgcccg acggcgagga tctcgtcgtg
     3781 acccatggcg atgcctgctt gccgaatatc atggtggaaa atggccgctt ttctggattc
     3841 atcgactgtg gccggctggg tgtggcggac cgctatcagg acatagcgtt ggctacccgt
     3901 gatattgctg aagagcttgg cggcgaatgg gctgaccgct tcctcgtgct ttacggtatc
     3961 gccgctcccg attcgcagcg catcgccttc tatcgccttc ttgacgagtt cttctgagcg
     4021 ggactctggg gttcgaaatg accgaccaag cgacgcccaa cctgccatca cgagatttcg
     4081 attccaccgc cgccttctat gaaaggttgg gcttcggaat cgttttccgg gacgccggct
     4141 ggatgatcct ccagcgcggg gatctcatgc tggagttctt cgcccacccc aacttgttta
     4201 ttgcagctta taatggttac aaataaagca atagcatcac aaatttcaca aataaagcat
     4261 ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct tatcatgtct
     4321 gtataccgtc gacctctagc tagagcttgg cgtaatcatg gtcatagctg tttcctgtgt
     4381 gaaattgtta tccgctcaca attccacaca acatacgagc cggaagcata aagtgtaaag
     4441 cctggggtgc ctaatgagtg agctaactca cattaattgc gttgcgctca ctgcccgctt
     4501 tccagtcggg aaacctgtcg tgccagctgc attaatgaat cggccaacgc gcggggagag
     4561 gcggtttgcg tattgggcgc tcttccgctt cctcgctcac tgactcgctg cgctcggtcg
     4621 ttcggctgcg gcgagcggta tcagctcact caaaggcggt aatacggtta tccacagaat
     4681 caggggataa cgcaggaaag aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta
     4741 aaaaggccgc gttgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa
     4801 atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc
     4861 cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt
     4921 ccgcctttct cccttcggga agcgtggcgc tttctcatag ctcacgctgt aggtatctca
     4981 gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg
     5041 accgctgcgc cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttat
     5101 cgccactggc agcagccact ggtaacagga ttagcagagc gaggtatgta ggcggtgcta
     5161 cagagttctt gaagtggtgg cctaactacg gctacactag aagaacagta tttggtatct
     5221 gcgctctgct gaagccagtt accttcggaa aaagagttgg tagctcttga tccggcaaac
     5281 aaaccaccgc tggtagcggt ggtttttttg tttgcaagca gcagattacg cgcagaaaaa
     5341 aaggatctca agaagatcct ttgatctttt ctacggggtc tgacgctcag tggaacgaaa
     5401 actcacgtta agggattttg gtcatgagat tatcaaaaag gatcttcacc tagatccttt
     5461 taaattaaaa atgaagtttt aaatcaatct aaagtatata tgagtaaact tggtctgaca
     5521 gttaccaatg cttaatcagt gaggcaccta tctcagcgat ctgtctattt cgttcatcca
     5581 tagttgcctg actccccgtc gtgtagataa ctacgatacg ggagggctta ccatctggcc
     5641 ccagtgctgc aatgataccg cgagacccac gctcaccggc tccagattta tcagcaataa
     5701 accagccagc cggaagggcc gagcgcagaa gtggtcctgc aactttatcc gcctccatcc
     5761 agtctattaa ttgttgccgg gaagctagag taagtagttc gccagttaat agtttgcgca
     5821 acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc gtcgtttggt atggcttcat
     5881 tcagctccgg ttcccaacga tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag
     5941 cggttagctc cttcggtcct ccgatcgttg tcagaagtaa gttggccgca gtgttatcac
     6001 tcatggttat ggcagcactg cataattctc ttactgtcat gccatccgta agatgctttt
     6061 ctgtgactgg tgagtactca accaagtcat tctgagaata gtgtatgcgg cgaccgagtt
     6121 gctcttgccc ggcgtcaata cgggataata ccgcgccaca tagcagaact ttaaaagtgc
     6181 tcatcattgg aaaacgttct tcggggcgaa aactctcaag gatcttaccg ctgttgagat
     6241 ccagttcgat gtaacccact cgtgcaccca actgatcttc agcatctttt actttcacca
     6301 gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc aaaaaaggga ataagggcga
     6361 cacggaaatg ttgaatactc atactcttcc tttttcaata ttattgaagc atttatcagg
     6421 gttattgtct catgagcgga tacatatttg aatgtattta gaaaaataaa caaatagggg
     6481 ttccgcgcac atttccccga aaagtgccac ctgacgtc
//
