LOCUS       sequence-399807-        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*40:06:01:01
FEATURES             Location/Qualifiers
     source          1..6452
                     /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(2043..2060)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2049..2273
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      2319..2747
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2406..2425)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2616..2637
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2756..2776)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        2761..3090
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      2941..3076
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3003..3022
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     CDS             3157..3951
                     /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(3211..3230)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3821..3840
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     polyA_signal    4125..4246
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4162..4181)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4216..4235
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4295..4311)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4295..4311)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4308..4330)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4319..4335
                     /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(4343..4349,4350..4367,4368..4373))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4388..4409
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4526..4543)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(4697..5285)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(4777..4796)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5456..6247,6248..6316))
                     /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     6079..6098
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(6317..6421)
                     /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 ccatgcgggt cacggcgccc cgaaccctcc tcctgctgct
      961 ctggggggca gtggccctga ccgagacctg ggctggctcc cactccatga ggtatttcca
     1021 cacctccgtg tcccggcccg gccgcgggga gccccgcttc atcaccgtgg gctacgtgga
     1081 cgacacgctg ttcgtgaggt tcgacagcga cgccacgagt ccgaggaagg agccgcgggc
     1141 gccatggata gagcaggagg ggccggagta ttgggaccgg gagacacaga tctccaagac
     1201 caacacacag acttaccgag agagcctgcg gaacctgcgc ggctactaca accagagcga
     1261 ggccgggtct cacacttggc agacgatgta tggctgcgac gtggggccgg acgggcgcct
     1321 cctccgcggg cataaccagt acgcctacga cggcaaggat tacatcgccc tgaacgagga
     1381 cctgcgctcc tggaccgccg cggacacggc ggctcagatc acccagcgca agtgggaggc
     1441 ggcccgtgtg gcggagcagc tgagagccta cctggagggc gagtgcgtgg agtggctccg
     1501 cagatacctg gagaacggga aggagacgct gcagcgcgcg gaccccccaa agacacacgt
     1561 gacccaccac cccatctctg accatgaggc caccctgagg tgctgggccc tgggcttcta
     1621 ccctgcggag atcacactga cctggcagcg ggatggcgag gaccaaactc aggacactga
     1681 gcttgtggag accagaccag caggagatag aaccttccag aagtgggcag ctgtggtggt
     1741 gccttctgga gaagagcaga gatacacatg ccatgtacag catgaggggc tgccgaagcc
     1801 cctcaccctg agatgggagc cgtcttccca gtccaccgtc cccatcgtgg gcattgttgc
     1861 tggcctggct gtcctagcag ttgtggtcat cggagctgtg gtcgctgctg tgatgtgtag
     1921 gaggaagagc tcaggtggaa aaggagggag ctactctcag gctgcgtgca gcgacagtgc
     1981 ccagggctct gatgtgtctc tcacagcttg atctagaggg cccgtttaaa cccgctgatc
     2041 agcctcgact gtgccttcta gttgccagcc atctgttgtt tgcccctccc ccgtgccttc
     2101 cttgaccctg gaaggtgcca ctcccactgt cctttcctaa taaaatgagg aaattgcatc
     2161 gcattgtctg agtaggtgtc attctattct ggggggtggg gtggggcagg acagcaaggg
     2221 ggaggattgg gaagacaata gcaggcatgc tggggatgcg gtgggctcta tggcttctga
     2281 ggcggaaaga accagctggg gctctagggg gtatccccac gcgccctgta gcggcgcatt
     2341 aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc
     2401 gcccgctcct ttcgctttct tcccttcctt tctcgccacg ttcgccggct ttccccgtca
     2461 agctctaaat cgggggctcc ctttagggtt ccgatttagt gctttacggc acctcgaccc
     2521 caaaaaactt gattagggtg atggttcacg tagtgggcca tcgccctgat agacggtttt
     2581 tcgccctttg acgttggagt ccacgttctt taatagtgga ctcttgttcc aaactggaac
     2641 aacactcaac cctatctcgg tctattcttt tgatttataa gggattttgc cgatttcggc
     2701 ctattggtta aaaaatgagc tgatttaaca aaaatttaac gcgaattaat tctgtggaat
     2761 gtgtgtcagt tagggtgtgg aaagtcccca ggctccccag caggcagaag tatgcaaagc
     2821 atgcatctca attagtcagc aaccaggtgt ggaaagtccc caggctcccc agcaggcaga
     2881 agtatgcaaa gcatgcatct caattagtca gcaaccatag tcccgcccct aactccgccc
     2941 atcccgcccc taactccgcc cagttccgcc cattctccgc cccatggctg actaattttt
     3001 tttatttatg cagaggccga ggccgcctct gcctctgagc tattccagaa gtagtgagga
     3061 ggcttttttg gaggcctagg cttttgcaaa aagctcccgg gagcttgtat atccattttc
     3121 ggatctgatc aagagacagg atgaggatcg tttcgcatga ttgaacaaga tggattgcac
     3181 gcaggttctc cggccgcttg ggtggagagg ctattcggct atgactgggc acaacagaca
     3241 atcggctgct ctgatgccgc cgtgttccgg ctgtcagcgc aggggcgccc ggttcttttt
     3301 gtcaagaccg acctgtccgg tgccctgaat gaactgcagg acgaggcagc gcggctatcg
     3361 tggctggcca cgacgggcgt tccttgcgca gctgtgctcg acgttgtcac tgaagcggga
     3421 agggactggc tgctattggg cgaagtgccg gggcaggatc tcctgtcatc tcaccttgct
     3481 cctgccgaga aagtatccat catggctgat gcaatgcggc ggctgcatac gcttgatccg
     3541 gctacctgcc cattcgacca ccaagcgaaa catcgcatcg agcgagcacg tactcggatg
     3601 gaagccggtc ttgtcgatca ggatgatctg gacgaagagc atcaggggct cgcgccagcc
     3661 gaactgttcg ccaggctcaa ggcgcgcatg cccgacggcg aggatctcgt cgtgacccat
     3721 ggcgatgcct gcttgccgaa tatcatggtg gaaaatggcc gcttttctgg attcatcgac
     3781 tgtggccggc tgggtgtggc ggaccgctat caggacatag cgttggctac ccgtgatatt
     3841 gctgaagagc ttggcggcga atgggctgac cgcttcctcg tgctttacgg tatcgccgct
     3901 cccgattcgc agcgcatcgc cttctatcgc cttcttgacg agttcttctg agcgggactc
     3961 tggggttcga aatgaccgac caagcgacgc ccaacctgcc atcacgagat ttcgattcca
     4021 ccgccgcctt ctatgaaagg ttgggcttcg gaatcgtttt ccgggacgcc ggctggatga
     4081 tcctccagcg cggggatctc atgctggagt tcttcgccca ccccaacttg tttattgcag
     4141 cttataatgg ttacaaataa agcaatagca tcacaaattt cacaaataaa gcattttttt
     4201 cactgcattc tagttgtggt ttgtccaaac tcatcaatgt atcttatcat gtctgtatac
     4261 cgtcgacctc tagctagagc ttggcgtaat catggtcata gctgtttcct gtgtgaaatt
     4321 gttatccgct cacaattcca cacaacatac gagccggaag cataaagtgt aaagcctggg
     4381 gtgcctaatg agtgagctaa ctcacattaa ttgcgttgcg ctcactgccc gctttccagt
     4441 cgggaaacct gtcgtgccag ctgcattaat gaatcggcca acgcgcgggg agaggcggtt
     4501 tgcgtattgg gcgctcttcc gcttcctcgc tcactgactc gctgcgctcg gtcgttcggc
     4561 tgcggcgagc ggtatcagct cactcaaagg cggtaatacg gttatccaca gaatcagggg
     4621 ataacgcagg aaagaacatg tgagcaaaag gccagcaaaa ggccaggaac cgtaaaaagg
     4681 ccgcgttgct ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac
     4741 gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg
     4801 gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct
     4861 ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgtaggtat ctcagttcgg
     4921 tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct
     4981 gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgac ttatcgccac
     5041 tggcagcagc cactggtaac aggattagca gagcgaggta tgtaggcggt gctacagagt
     5101 tcttgaagtg gtggcctaac tacggctaca ctagaagaac agtatttggt atctgcgctc
     5161 tgctgaagcc agttaccttc ggaaaaagag ttggtagctc ttgatccggc aaacaaacca
     5221 ccgctggtag cggtggtttt tttgtttgca agcagcagat tacgcgcaga aaaaaaggat
     5281 ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc tcagtggaac gaaaactcac
     5341 gttaagggat tttggtcatg agattatcaa aaaggatctt cacctagatc cttttaaatt
     5401 aaaaatgaag ttttaaatca atctaaagta tatatgagta aacttggtct gacagttacc
     5461 aatgcttaat cagtgaggca cctatctcag cgatctgtct atttcgttca tccatagttg
     5521 cctgactccc cgtcgtgtag ataactacga tacgggaggg cttaccatct ggccccagtg
     5581 ctgcaatgat accgcgagac ccacgctcac cggctccaga tttatcagca ataaaccagc
     5641 cagccggaag ggccgagcgc agaagtggtc ctgcaacttt atccgcctcc atccagtcta
     5701 ttaattgttg ccgggaagct agagtaagta gttcgccagt taatagtttg cgcaacgttg
     5761 ttgccattgc tacaggcatc gtggtgtcac gctcgtcgtt tggtatggct tcattcagct
     5821 ccggttccca acgatcaagg cgagttacat gatcccccat gttgtgcaaa aaagcggtta
     5881 gctccttcgg tcctccgatc gttgtcagaa gtaagttggc cgcagtgtta tcactcatgg
     5941 ttatggcagc actgcataat tctcttactg tcatgccatc cgtaagatgc ttttctgtga
     6001 ctggtgagta ctcaaccaag tcattctgag aatagtgtat gcggcgaccg agttgctctt
     6061 gcccggcgtc aatacgggat aataccgcgc cacatagcag aactttaaaa gtgctcatca
     6121 ttggaaaacg ttcttcgggg cgaaaactct caaggatctt accgctgttg agatccagtt
     6181 cgatgtaacc cactcgtgca cccaactgat cttcagcatc ttttactttc accagcgttt
     6241 ctgggtgagc aaaaacagga aggcaaaatg ccgcaaaaaa gggaataagg gcgacacgga
     6301 aatgttgaat actcatactc ttcctttttc aatattattg aagcatttat cagggttatt
     6361 gtctcatgag cggatacata tttgaatgta tttagaaaaa taaacaaata ggggttccgc
     6421 gcacatttcc ccgaaaagtg ccacctgacg tc
//
