LOCUS       sequence-399853-        6461 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 6461)
  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 6461)
  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*34:01:01
FEATURES             Location/Qualifiers
     source          1..6461
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(9..29)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        14..343
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      194..329
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     256..275
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             410..1204
                     /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(464..483)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     1074..1093
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    1378..1499
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(1415..1434)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     1469..1488
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(1548..1564)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1548..1564)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1561..1583)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1572..1588
                     /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(1596..1602,1603..1620,1621..1626))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1641..1662
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1779..1796)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1950..2538)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2030..2049)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2709..3500,3501..3569))
                     /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     3332..3351
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3570..3674)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     complement(3749..3768)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     enhancer        3940..4319
                     /label=CMV enhancer
                     /note="human cytomegalovirus immediate early enhancer"
     promoter        4320..4523
                     /label=CMV promoter
                     /note="human cytomegalovirus (CMV) immediate early 
                     promoter"
     primer_bind     4474..4494
                     /label=CMV-F
                     /note="Human CMV immediate early promoter, forward primer"
     primer_bind     4568..4587
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        4568..4586
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     regulatory      4622..4631
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     primer_bind     complement(5757..5774)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    5763..5987
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      6033..6461
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6120..6139)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     6330..6351
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
ORIGIN
        1 aattctgtgg aatgtgtgtc agttagggtg tggaaagtcc ccaggctccc cagcaggcag
       61 aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc
      121 cccagcaggc agaagtatgc aaagcatgca tctcaattag tcagcaacca tagtcccgcc
      181 cctaactccg cccatcccgc ccctaactcc gcccagttcc gcccattctc cgccccatgg
      241 ctgactaatt ttttttattt atgcagaggc cgaggccgcc tctgcctctg agctattcca
      301 gaagtagtga ggaggctttt ttggaggcct aggcttttgc aaaaagctcc cgggagcttg
      361 tatatccatt ttcggatctg atcaagagac aggatgagga tcgtttcgca tgattgaaca
      421 agatggattg cacgcaggtt ctccggccgc ttgggtggag aggctattcg gctatgactg
      481 ggcacaacag acaatcggct gctctgatgc cgccgtgttc cggctgtcag cgcaggggcg
      541 cccggttctt tttgtcaaga ccgacctgtc cggtgccctg aatgaactgc aggacgaggc
      601 agcgcggcta tcgtggctgg ccacgacggg cgttccttgc gcagctgtgc tcgacgttgt
      661 cactgaagcg ggaagggact ggctgctatt gggcgaagtg ccggggcagg atctcctgtc
      721 atctcacctt gctcctgccg agaaagtatc catcatggct gatgcaatgc ggcggctgca
      781 tacgcttgat ccggctacct gcccattcga ccaccaagcg aaacatcgca tcgagcgagc
      841 acgtactcgg atggaagccg gtcttgtcga tcaggatgat ctggacgaag agcatcaggg
      901 gctcgcgcca gccgaactgt tcgccaggct caaggcgcgc atgcccgacg gcgaggatct
      961 cgtcgtgacc catggcgatg cctgcttgcc gaatatcatg gtggaaaatg gccgcttttc
     1021 tggattcatc gactgtggcc ggctgggtgt ggcggaccgc tatcaggaca tagcgttggc
     1081 tacccgtgat attgctgaag agcttggcgg cgaatgggct gaccgcttcc tcgtgcttta
     1141 cggtatcgcc gctcccgatt cgcagcgcat cgccttctat cgccttcttg acgagttctt
     1201 ctgagcggga ctctggggtt cgaaatgacc gaccaagcga cgcccaacct gccatcacga
     1261 gatttcgatt ccaccgccgc cttctatgaa aggttgggct tcggaatcgt tttccgggac
     1321 gccggctgga tgatcctcca gcgcggggat ctcatgctgg agttcttcgc ccaccccaac
     1381 ttgtttattg cagcttataa tggttacaaa taaagcaata gcatcacaaa tttcacaaat
     1441 aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa tgtatcttat
     1501 catgtctgta taccgtcgac ctctagctag agcttggcgt aatcatggtc atagctgttt
     1561 cctgtgtgaa attgttatcc gctcacaatt ccacacaaca tacgagccgg aagcataaag
     1621 tgtaaagcct ggggtgccta atgagtgagc taactcacat taattgcgtt gcgctcactg
     1681 cccgctttcc agtcgggaaa cctgtcgtgc cagctgcatt aatgaatcgg ccaacgcgcg
     1741 gggagaggcg gtttgcgtat tgggcgctct tccgcttcct cgctcactga ctcgctgcgc
     1801 tcggtcgttc ggctgcggcg agcggtatca gctcactcaa aggcggtaat acggttatcc
     1861 acagaatcag gggataacgc aggaaagaac atgtgagcaa aaggccagca aaaggccagg
     1921 aaccgtaaaa aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat
     1981 cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag
     2041 gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga
     2101 tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgtagg
     2161 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
     2221 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac
     2281 gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag gtatgtaggc
     2341 ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag aacagtattt
     2401 ggtatctgcg ctctgctgaa gccagttacc ttcggaaaaa gagttggtag ctcttgatcc
     2461 ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc
     2521 agaaaaaaag gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg
     2581 aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat cttcacctag
     2641 atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg
     2701 tctgacagtt accaatgctt aatcagtgag gcacctatct cagcgatctg tctatttcgt
     2761 tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca
     2821 tctggcccca gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca
     2881 gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac tttatccgcc
     2941 tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt
     3001 ttgcgcaacg ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc gtttggtatg
     3061 gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc
     3121 aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg
     3181 ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc atccgtaaga
     3241 tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga
     3301 ccgagttgct cttgcccggc gtcaatacgg gataataccg cgccacatag cagaacttta
     3361 aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg
     3421 ttgagatcca gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact
     3481 ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata
     3541 agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt
     3601 tatcagggtt attgtctcat gagcggatac atatttgaat gtatttagaa aaataaacaa
     3661 ataggggttc cgcgcacatt tccccgaaaa gtgccacctg acgtcgacgg atcgggagat
     3721 ctcccgatcc cctatggtgc actctcagta caatctgctc tgatgccgca tagttaagcc
     3781 agtatctgct ccctgcttgt gtgttggagg tcgctgagta gtgcgcgagc aaaatttaag
     3841 ctacaacaag gcaaggcttg accgacaatt gcatgaagaa tctgcttagg gttaggcgtt
     3901 ttgcgctgct tcgcgatgta cgggccagat atacgcgttg acattgatta ttgactagtt
     3961 attaatagta atcaattacg gggtcattag ttcatagccc atatatggag ttccgcgtta
     4021 cataacttac ggtaaatggc ccgcctggct gaccgcccaa cgacccccgc ccattgacgt
     4081 caataatgac gtatgttccc atagtaacgc caatagggac tttccattga cgtcaatggg
     4141 tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat atgccaagta
     4201 cgccccctat tgacgtcaat gacggtaaat ggcccgcctg gcattatgcc cagtacatga
     4261 ccttatggga ctttcctact tggcagtaca tctacgtatt agtcatcgct attaccatgg
     4321 tgatgcggtt ttggcagtac atcaatgggc gtggatagcg gtttgactca cggggatttc
     4381 caagtctcca ccccattgac gtcaatggga gtttgttttg gcaccaaaat caacgggact
     4441 ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg cgtgtacggt
     4501 gggaggtcta tataagcaga gctctctggc taactagaga acccactgct tactggctta
     4561 tcgaaattaa tacgactcac tatagggaga cccaagctgg ctagcgttta aacttaagct
     4621 tgccaccatg gccatcatgg cgccccgaac cctcgtcctg ctactctcgg gggccctggc
     4681 cctgacccag acctgggcgg gctcccactc catgaggtat ttctacacct ccgtgtcccg
     4741 gcccggccgc ggggagcccc gcttcatcgc cgtgggctac gtggacgaca cgcagttcgt
     4801 gcggttcgac agcgacgccg cgagccagag gatggagccg cgggcgccgt ggatagagca
     4861 ggaggggccg gagtattggg accggaacac acggaaagtg aaggcccagt cacagactga
     4921 ccgagtggac ctggggaccc tgcgcggcta ctacaaccag agcgaggacg gttctcacac
     4981 catccagagg atgtatggct gcgacgtggg gccggacggg cgcttcctcc gcgggtacca
     5041 gcaggacgct tacgacggca aggattacat cgccctgaac gaggacctgc gctcttggac
     5101 cgcggcggac atggcggctc agatcaccca gcgcaagtgg gagacggccc atgaggcgga
     5161 gcagtggaga gcctacctgg agggcacgtg cgtggagtgg ctccgcagat acctggagaa
     5221 cgggaaggag acgctgcagc gcacggacgc ccccaagaca catatgactc accacgctgt
     5281 ctctgaccat gaggccaccc tgaggtgctg ggccctgagc ttctaccctg cggagatcac
     5341 actgacctgg cagcgggatg gggaggacca gacccaggac acggagctcg tggagaccag
     5401 gcctgcaggg gatggaacct tccagaagtg ggcgtctgtg gtggtgcctt ctggacagga
     5461 gcagagatac acctgccatg tgcagcatga gggtctgccc aagcccctca ccctgagatg
     5521 ggagccgtct tcccagccca ccatccccat cgtgggcatc cttgctggcc tggttctctt
     5581 tggagctgtg atcgctggag ctgtggtcgc tgctgtgatg tggaggagga agagctcaga
     5641 tagaaaagga gggagctact ctcaggctgc aagcagtgac agtgcccagg gctctgatat
     5701 gtctctcaca gcttgtaaag tgtgatctag agggcccgtt taaacccgct gatcagcctc
     5761 gactgtgcct tctagttgcc agccatctgt tgtttgcccc tcccccgtgc cttccttgac
     5821 cctggaaggt gccactccca ctgtcctttc ctaataaaat gaggaaattg catcgcattg
     5881 tctgagtagg tgtcattcta ttctgggggg tggggtgggg caggacagca agggggagga
     5941 ttgggaagac aatagcaggc atgctgggga tgcggtgggc tctatggctt ctgaggcgga
     6001 aagaaccagc tggggctcta gggggtatcc ccacgcgccc tgtagcggcg cattaagcgc
     6061 ggcgggtgtg gtggttacgc gcagcgtgac cgctacactt gccagcgccc tagcgcccgc
     6121 tcctttcgct ttcttccctt cctttctcgc cacgttcgcc ggctttcccc gtcaagctct
     6181 aaatcggggg ctccctttag ggttccgatt tagtgcttta cggcacctcg accccaaaaa
     6241 acttgattag ggtgatggtt cacgtagtgg gccatcgccc tgatagacgg tttttcgccc
     6301 tttgacgttg gagtccacgt tctttaatag tggactcttg ttccaaactg gaacaacact
     6361 caaccctatc tcggtctatt cttttgattt ataagggatt ttgccgattt cggcctattg
     6421 gttaaaaaat gagctgattt aacaaaaatt taacgcgaat t
//
