LOCUS       sequence-399943-        6467 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 6467)
  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 6467)
  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*11:01:01:01
FEATURES             Location/Qualifiers
     source          1..6467
                     /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      917..926
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     primer_bind     complement(2058..2075)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2064..2288
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2334..2762
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2421..2440)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2631..2652
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2771..2791)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2776..3105
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2956..3091
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3018..3037
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3172..3966
                     /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(3226..3245)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3836..3855
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4140..4261
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4177..4196)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4231..4250
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4310..4326)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4310..4326)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4323..4345)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4334..4350
                     /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(4358..4364,4365..4382,4383..4388))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4403..4424
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4541..4558)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4712..5300)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4792..4811)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5471..6262,6263..6331))
                     /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     6094..6113
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6332..6436)
                     /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 aagcttgcca ccatggccgt catggcgccc cgaaccctcc tcctgctact
      961 ctcgggggcc ctggccctga cccagacctg ggcgggctcc cactccatga ggtatttcta
     1021 cacctccgtg tcccggcccg gccgcgggga gccccgcttc atcgccgtgg gctacgtgga
     1081 cgacacgcag ttcgtgcggt tcgacagcga cgccgcgagc cagaggatgg agccgcgggc
     1141 gccgtggata gagcaggagg ggccggagta ttgggaccag gagacacgga atgtgaaggc
     1201 ccagtcacag actgaccgag tggacctggg gaccctgcgc ggctactaca accagagcga
     1261 ggacggttct cacaccatcc agataatgta tggctgcgac gtggggccgg acgggcgctt
     1321 cctccgcggg taccggcagg acgcctacga cggcaaggat tacatcgccc tgaacgagga
     1381 cctgcgctct tggaccgcgg cggacatggc agctcagatc accaagcgca agtgggaggc
     1441 ggcccatgcg gcggagcagc agagagccta cctggagggc cggtgcgtgg agtggctccg
     1501 cagatacctg gagaacggga aggagacgct gcagcgcacg gaccccccca agacacatat
     1561 gacccaccac cccatctctg accatgaggc caccctgagg tgctgggccc tgggcttcta
     1621 ccctgcggag atcacactga cctggcagcg ggatggggag gaccagaccc aggacacgga
     1681 gctcgtggag accaggcctg caggggatgg aaccttccag aagtgggcgg ctgtggtggt
     1741 gccttctgga gaggagcaga gatacacctg ccatgtgcag catgagggtc tgcccaagcc
     1801 cctcaccctg agatgggagc tgtcttccca gcccaccatc cccatcgtgg gcatcattgc
     1861 tggcctggtt ctccttggag ctgtgatcac tggagctgtg gtcgctgccg tgatgtggag
     1921 gaggaagagc tcagatagaa aaggagggag ttacactcag gctgcaagca gtgacagtgc
     1981 ccagggctct gatgtgtctc tcacagcttg taaagtgtga tgataatcta gagggcccgt
     2041 ttaaacccgc tgatcagcct cgactgtgcc ttctagttgc cagccatctg ttgtttgccc
     2101 ctcccccgtg ccttccttga ccctggaagg tgccactccc actgtccttt cctaataaaa
     2161 tgaggaaatt gcatcgcatt gtctgagtag gtgtcattct attctggggg gtggggtggg
     2221 gcaggacagc aagggggagg attgggaaga caatagcagg catgctgggg atgcggtggg
     2281 ctctatggct tctgaggcgg aaagaaccag ctggggctct agggggtatc cccacgcgcc
     2341 ctgtagcggc gcattaagcg cggcgggtgt ggtggttacg cgcagcgtga ccgctacact
     2401 tgccagcgcc ctagcgcccg ctcctttcgc tttcttccct tcctttctcg ccacgttcgc
     2461 cggctttccc cgtcaagctc taaatcgggg gctcccttta gggttccgat ttagtgcttt
     2521 acggcacctc gaccccaaaa aacttgatta gggtgatggt tcacgtagtg ggccatcgcc
     2581 ctgatagacg gtttttcgcc ctttgacgtt ggagtccacg ttctttaata gtggactctt
     2641 gttccaaact ggaacaacac tcaaccctat ctcggtctat tcttttgatt tataagggat
     2701 tttgccgatt tcggcctatt ggttaaaaaa tgagctgatt taacaaaaat ttaacgcgaa
     2761 ttaattctgt ggaatgtgtg tcagttaggg tgtggaaagt ccccaggctc cccagcaggc
     2821 agaagtatgc aaagcatgca tctcaattag tcagcaacca ggtgtggaaa gtccccaggc
     2881 tccccagcag gcagaagtat gcaaagcatg catctcaatt agtcagcaac catagtcccg
     2941 cccctaactc cgcccatccc gcccctaact ccgcccagtt ccgcccattc tccgccccat
     3001 ggctgactaa ttttttttat ttatgcagag gccgaggccg cctctgcctc tgagctattc
     3061 cagaagtagt gaggaggctt ttttggaggc ctaggctttt gcaaaaagct cccgggagct
     3121 tgtatatcca ttttcggatc tgatcaagag acaggatgag gatcgtttcg catgattgaa
     3181 caagatggat tgcacgcagg ttctccggcc gcttgggtgg agaggctatt cggctatgac
     3241 tgggcacaac agacaatcgg ctgctctgat gccgccgtgt tccggctgtc agcgcagggg
     3301 cgcccggttc tttttgtcaa gaccgacctg tccggtgccc tgaatgaact gcaggacgag
     3361 gcagcgcggc tatcgtggct ggccacgacg ggcgttcctt gcgcagctgt gctcgacgtt
     3421 gtcactgaag cgggaaggga ctggctgcta ttgggcgaag tgccggggca ggatctcctg
     3481 tcatctcacc ttgctcctgc cgagaaagta tccatcatgg ctgatgcaat gcggcggctg
     3541 catacgcttg atccggctac ctgcccattc gaccaccaag cgaaacatcg catcgagcga
     3601 gcacgtactc ggatggaagc cggtcttgtc gatcaggatg atctggacga agagcatcag
     3661 gggctcgcgc cagccgaact gttcgccagg ctcaaggcgc gcatgcccga cggcgaggat
     3721 ctcgtcgtga cccatggcga tgcctgcttg ccgaatatca tggtggaaaa tggccgcttt
     3781 tctggattca tcgactgtgg ccggctgggt gtggcggacc gctatcagga catagcgttg
     3841 gctacccgtg atattgctga agagcttggc ggcgaatggg ctgaccgctt cctcgtgctt
     3901 tacggtatcg ccgctcccga ttcgcagcgc atcgccttct atcgccttct tgacgagttc
     3961 ttctgagcgg gactctgggg ttcgaaatga ccgaccaagc gacgcccaac ctgccatcac
     4021 gagatttcga ttccaccgcc gccttctatg aaaggttggg cttcggaatc gttttccggg
     4081 acgccggctg gatgatcctc cagcgcgggg atctcatgct ggagttcttc gcccacccca
     4141 acttgtttat tgcagcttat aatggttaca aataaagcaa tagcatcaca aatttcacaa
     4201 ataaagcatt tttttcactg cattctagtt gtggtttgtc caaactcatc aatgtatctt
     4261 atcatgtctg tataccgtcg acctctagct agagcttggc gtaatcatgg tcatagctgt
     4321 ttcctgtgtg aaattgttat ccgctcacaa ttccacacaa catacgagcc ggaagcataa
     4381 agtgtaaagc ctggggtgcc taatgagtga gctaactcac attaattgcg ttgcgctcac
     4441 tgcccgcttt ccagtcggga aacctgtcgt gccagctgca ttaatgaatc ggccaacgcg
     4501 cggggagagg cggtttgcgt attgggcgct cttccgcttc ctcgctcact gactcgctgc
     4561 gctcggtcgt tcggctgcgg cgagcggtat cagctcactc aaaggcggta atacggttat
     4621 ccacagaatc aggggataac gcaggaaaga acatgtgagc aaaaggccag caaaaggcca
     4681 ggaaccgtaa aaaggccgcg ttgctggcgt ttttccatag gctccgcccc cctgacgagc
     4741 atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc
     4801 aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg
     4861 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta
     4921 ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
     4981 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac
     5041 acgacttatc gccactggca gcagccactg gtaacaggat tagcagagcg aggtatgtag
     5101 gcggtgctac agagttcttg aagtggtggc ctaactacgg ctacactaga agaacagtat
     5161 ttggtatctg cgctctgctg aagccagtta ccttcggaaa aagagttggt agctcttgat
     5221 ccggcaaaca aaccaccgct ggtagcggtg gtttttttgt ttgcaagcag cagattacgc
     5281 gcagaaaaaa aggatctcaa gaagatcctt tgatcttttc tacggggtct gacgctcagt
     5341 ggaacgaaaa ctcacgttaa gggattttgg tcatgagatt atcaaaaagg atcttcacct
     5401 agatcctttt aaattaaaaa tgaagtttta aatcaatcta aagtatatat gagtaaactt
     5461 ggtctgacag ttaccaatgc ttaatcagtg aggcacctat ctcagcgatc tgtctatttc
     5521 gttcatccat agttgcctga ctccccgtcg tgtagataac tacgatacgg gagggcttac
     5581 catctggccc cagtgctgca atgataccgc gagacccacg ctcaccggct ccagatttat
     5641 cagcaataaa ccagccagcc ggaagggccg agcgcagaag tggtcctgca actttatccg
     5701 cctccatcca gtctattaat tgttgccggg aagctagagt aagtagttcg ccagttaata
     5761 gtttgcgcaa cgttgttgcc attgctacag gcatcgtggt gtcacgctcg tcgtttggta
     5821 tggcttcatt cagctccggt tcccaacgat caaggcgagt tacatgatcc cccatgttgt
     5881 gcaaaaaagc ggttagctcc ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag
     5941 tgttatcact catggttatg gcagcactgc ataattctct tactgtcatg ccatccgtaa
     6001 gatgcttttc tgtgactggt gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc
     6061 gaccgagttg ctcttgcccg gcgtcaatac gggataatac cgcgccacat agcagaactt
     6121 taaaagtgct catcattgga aaacgttctt cggggcgaaa actctcaagg atcttaccgc
     6181 tgttgagatc cagttcgatg taacccactc gtgcacccaa ctgatcttca gcatctttta
     6241 ctttcaccag cgtttctggg tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa
     6301 taagggcgac acggaaatgt tgaatactca tactcttcct ttttcaatat tattgaagca
     6361 tttatcaggg ttattgtctc atgagcggat acatatttga atgtatttag aaaaataaac
     6421 aaataggggt tccgcgcaca tttccccgaa aagtgccacc tgacgtc
//
