LOCUS       sequence-491552-        8561 bp    DNA     circular SYN 04-NOV-2025
DEFINITION  Proximity-labeling proteomics with SHP2.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 8561)
  AUTHORS   van Vlimmeren AE, Tang LC, Jiang Z, Iyer A, Voleti R, Krismer K, 
            Gaublomme JT, Jovanovic M, Shah NH
  TITLE     Proximity-labeling proteomics reveals remodeled interactomes and 
            altered localization of pathogenic SHP2 variants.
  JOURNAL   bioRxiv [Preprint]. 2025 Mar 21:2025.02.26.640373. doi: 
            10.1101/2025.02.26.640373.
  PUBMED    40661614
REFERENCE   2  (bases 1 to 8561)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Nov 4, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "bioRxiv 
            [Preprint]. 2025 Mar 21:2025.02.26.640373. doi: 
            10.1101/2025.02.26.640373."
COMMENT     Sequence Label: pEF myc-SHP2(R138Q)-TurboID
FEATURES             Location/Qualifiers
     source          1..8561
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     228..248
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     rep_origin      complement(257..685)
                     /direction=LEFT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(367..388)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     579..598
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     polyA_signal    731..955
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     primer_bind     944..961
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     CDS             complement(987..1013)
                     /codon_start=1
                     /product="nuclear export signal from the HIV Rev protein 
                     (Fischer et al., 1995)"
                     /label=NES
                     /translation="LPPLERLTL"
     CDS             complement(1020..1976)
                     /codon_start=1
                     /product="mutant of the E. coli biotin ligase BioID 
                     engineered for improved catalytic efficiency (Branon et 
                     al., 2018)"
                     /label=TurboID
                     /translation="KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDW
                     GVDVFTVPGKGYSLPEPIPLLNAKQILGQLDGGSVAVLPVVDSTNQYLLDRIGELKSGD
                     ACIAEYQQAGRGSRGRKWFSPFGANLYLSMFWRLKRGPAAIGLGPVIGIVMAEALRKLG
                     ADKVRVKWPNDLYLQDRKLAGILVELAGITGDAAQIVIGAGINVAMRRVEESVVNQGWI
                     TLQEAGINLDRNTLAATLIRELRAALELFEQEGLAPYLPRWEKLDNFINRPVKLIIGDK
                     EIFGISRGIDKQGALLLEQDGVIKPWMGGEISLRSAEK"
     CDS             complement(3774..3803)
                     /codon_start=1
                     /product="Myc (human c-Myc proto-oncogene) epitope tag"
                     /label=Myc
                     /translation="EQKLISEEDL"
     primer_bind     complement(3924..3943)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(3925..3943)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     promoter        complement(3960..5138)
                     /label=EF-1-alpha promoter
                     /note="strong constitutive promoter for human elongation 
                     factor EF-1-alpha"
     intron          3969..4907
                     /label=EF-1-alpha intron A
                     /note="intron upstream of the start codon of human 
                     EF-1-alpha"
     primer_bind     complement(3992..4012)
                     /label=EF1a-F
                     /note="Human elongation factor-1a promoter, forward primer"
     primer_bind     5426..5445
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     promoter        5520..5624
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5625..5693,5694..6485)
                     /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"
     rep_origin      6656..7244
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7145..7164
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7387..7404
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    7521..7542
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(7557..7562,7563..7580,7581..7587)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    7595..7611
                     /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)."
     primer_bind     7600..7622
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     7619..7635
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     7619..7635
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     polyA_signal    7684..7805
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(7695..7714)
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     7749..7768
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     CDS             complement(7963..8361)
                     /codon_start=1
                     /gene="Aspergillus terreus BSD"
                     /product="blasticidin S deaminase"
                     /label=BSD
                     /note="confers resistance to blasticidin"
                     /translation="MAKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTG
                     VNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGI
                     KAIVKDSDGQPTAVGIRELLPSGYVWEG"
     promoter        complement(8380..8427)
                     /label=EM7 promoter
                     /note="synthetic bacterial promoter "
     promoter        complement(join(8475..8561,1..243))
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      join(8489..8561,1..63)
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     complement(join(8543..8561,1))
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
ORIGIN
        1 aaaaaaaatt agtcagccat ggggcggaga atgggcggaa ctgggcggag ttaggggcgg
       61 gatgggcgga gttaggggcg ggactatggt tgctgactaa ttgagatgca tgctttgcat
      121 acttctgcct gctggggagc ctggggactt tccacacctg gttgctgact aattgagatg
      181 catgctttgc atacttctgc ctgctgggga gcctggggac tttccacacc ctaactgaca
      241 cacattccac agaattaatt cgcgttaaat ttttgttaaa tcagctcatt ttttaaccaa
      301 taggccgaaa tcggcaaaat cccttataaa tcaaaagaat agaccgagat agggttgagt
      361 gttgttccag tttggaacaa gagtccacta ttaaagaacg tggactccaa cgtcaaaggg
      421 cgaaaaaccg tctatcaggg cgatggccca ctacgtgaac catcacccta atcaagtttt
      481 ttggggtcga ggtgccgtaa agcactaaat cggaacccta aagggagccc ccgatttaga
      541 gcttgacggg gaaagccggc gaacgtggcg agaaaggaag ggaagaaagc gaaaggagcg
      601 ggcgctaggg cgctggcaag tgtagcggtc acgctgcgcg taaccaccac acccgccgcg
      661 cttaatgcgc cgctacaggg cgcgtgggga taccccctag agccccagct ggttctttcc
      721 gcctcagaag ccatagagcc caccgcatcc ccagcatgcc tgctattgtc ttcccaatcc
      781 tcccccttgc tgtcctgccc caccccaccc cccagaatag aatgacacct actcagacaa
      841 tgcgatgcaa tttcctcatt ttattaggaa aggacagtgg gagtggcacc ttccagggtc
      901 aaggaaggca cgggggaggg gcaaacaaca gatggctggc aactagaagg cacagtcgag
      961 gctgatcagc gggtttaaac ttagtccagg gtcaggcgct ccaggggagg cagctgcagc
     1021 ttttcggcag accgcagact gatttctccg cccatccagg gtttgataac tccgtcctgt
     1081 tccagcagca gggctccctg tttatcaatc ccccggctaa tcccgaaaat ctctttgtcc
     1141 ccaatgatca gcttcacggg tctattgatg aagttatcca gcttctccca ccgtggcaga
     1201 tatggagcca ggccttcctg ctcgaacagt tccagggctg cccgcagctc tcggatcagc
     1261 gtagcggcca gagtattcct gtccaggtta atccctgctt cctgcagtgt gatccagccc
     1321 tgattgacca cgctttcctc cacgcgcctc atagccacgt taatcccggc gccaatgacg
     1381 atctgtgcag catcgcctgt tattccggcc agctccacca ggatgcctgc cagctttcta
     1441 tcctgcagat acaggtcatt gggccatttg actcgcacct tgtctgctcc cagctttcgc
     1501 agcgcttctg ccatgacaat tccgatgacc gggcccaggc cgattgctgc tggtccccgc
     1561 ttcaggcgcc aaaacatact caggtacagg ttagctccaa aaggagagaa ccatttcctc
     1621 cctctgcttc ctctccctgc ctgctgatat tctgcaatgc aagcatcccc actcttcagc
     1681 tcgccgattc gatccagcag gtactgattg gtggagtcga ccacaggcag gactgccacg
     1741 ctcccgccgt ccagctgtcc cagaatctgt ttagcgttca gcagcgggat aggctcgggc
     1801 agagagtagc cctttccggg cacggtgaac acgtccacgc cccagtcgcg cagagtctga
     1861 atgtgcttgt tgatagcggc cctggacatg cccagggttt ctcccagctg ttcgccacta
     1921 tggaactcgc cattagccag gagagcgatc agcttcagag gcacagtatt gtcttttctg
     1981 aaacttttct gctgttgcat caggcccacg ttttcataga ctctagcact gtcttctctc
     2041 atttctgcac agggtggcgt tggagtacaa ggcgggagag ggctctgatc tccactcgtc
     2101 tggtccgcta gagaatactt aatatttgta tattcgtgcc ctttcctctt gcttttctgc
     2161 tcttcttcaa tcctgcgctg tagtgtttca atataatgct ggaccgccat atagataaat
     2221 cggtactgtg cttctgtctg gaccatccct gacctctgag accgcaccat ctggatggtt
     2281 ttgggaacgt caatatcgca gtcaacacct ttctctctga tgatgtcaat aagaatatca
     2341 atcacaatga acgtccctgt ccggccaatt ccagcactgc agtgcaccac gaccggccct
     2401 gcatccatga tgctctcctg cttatggtgc acctcctcca ggaagtccag cacgccccca
     2461 gggtcgctgg gcacgccgtg gtccggccag gtccgaaagt ggtattgcca gaccgttctc
     2521 tccgtattcc cttgtccaac ctttgaaagt ttaagttctc ttagcgtata gtcatgagcg
     2581 gcgctttctt tgacgttcct aacacgcatg acgccatatt cttttagagc atactcatca
     2641 ggccagtatt tgacacattt actctttcct ctctccactt ctttcgttgt catgacaatc
     2701 actcgggagt tttcttggaa caccatccgc caaaagtcat tcaccgtgtt ttgcaggcag
     2761 ccttgtgtgg caatgtaact ctttttgggc tttgaattgt tgcacttggt ttcaaattca
     2821 ggcatgatga tatttgcatt gatgtaatct gaaacaggct cattgggatc accatcgtgt
     2881 aggacaaccc tggtatgatc aaagggcagg atgtttttat atctattttt gtttttgttt
     2941 tcttgccttt gaccctcttt tcggctgtag agaagtttgc actcctgttg ttgtagtgtc
     3001 tcaaattctt cccaaaagcc ttgtttgact ttatctgtgg tctcagctaa tttgcttagt
     3061 tctcgaactc tgctttctat ttcagcagca tttatacgag tcgtgttaag gggctgcttg
     3121 agttgtagta ctgtacccaa tgtttccacc ataggattct tcttataatg ttccacaaga
     3181 tctgtcaaag aatcaaaccg ttctcctcca ccaacgtcgt atttcagttc ctgacagcga
     3241 atcataacat gggtcacttt agacttgccg tcattgctct cccctttgtc atcaccagtg
     3301 cgcacagaaa gaacaaaatc tccagggtgg ctctggctct cttgtacaag aaaactacca
     3361 tgttttcctt tttcagttaa taatttctct gcttctttcc cagagagatg tccatgaaac
     3421 cacctttcag aggtaggatc tgcacagttc agaggatatt taagctcaat gacatctcca
     3481 ttcttctctt ttaattgccc gtgatgttcc atgtaatact ggaccaactc agccaaagtg
     3541 gcaaatttct cccctccata caggtcatag taatcaccag tgttctgaat cttgatgtgg
     3601 gtgacagctc catttcttct aacggaaagt gtgaagtctc cagggttact tttactaggc
     3661 cttgccaaaa aactgccatc aactcctctt gtcaacagta ggttttctgc ctccacacca
     3721 gtgatatttg ggtgaaacca tctccgcgat gtcatctgcc cagactgccc tcccagatcc
     3781 tcttctgaga tgagtttttg ttccatggtg aagggccctc tagactcgag cggccgccac
     3841 tgtgctggat atctgcagaa ttccaccaca ctggactagt ggatccgagc tcggtaccaa
     3901 gcttacctag ccagcttggg tctccctata gtgagtcgta ttagtaccaa gctaattcct
     3961 cacgacacct gaaatggaag aaaaaaactt tgaaccactg tctgaggctt gagaatgaac
     4021 caagatccaa actcaaaaag ggcaaattcc aaggagaatt acatcaagtg ccaagctggc
     4081 ctaacttcag tctccaccca ctcagtgtgg ggaaactcca tcgcataaaa cccctccccc
     4141 caacctaaag acgacgtact ccaaaagctc gagaactaat cgaggtgcct ggacggcgcc
     4201 cggtactccg tggagtcaca tgaagcgacg gctgaggacg gaaaggccct tttcctttgt
     4261 gtgggtgact cacccgcccg ctctcccgag cgccgcgtcc tccattttga gctccctgca
     4321 gcagggccgg gaagcggcca tctttccgct cacgcaactg gtgccgaccg ggccagcctt
     4381 gccgcccagg gcggggcgat acacggcggc gcgaggccag gcaccagagc aggccggcca
     4441 gcttgagact acccccgtcc gattctcggt ggccgcgctc gcaggccccg cctcgccgaa
     4501 catgtgcgct gggacgcacg ggccccgtcg ccgcccgcgg ccccaaaaac cgaaatacca
     4561 gtgtgcagat cttggcccgc atttacaaga ctatcttgcc agaaaaaaag cgtcgcagca
     4621 ggtcatcaaa aattttaaat ggctagagac ttatcgaaag cagcgagaca ggcgcgaagg
     4681 tgccaccaga ttcgcacgcg gcggccccag cgcccaggcc aggcctcaac tcaagcacga
     4741 ggcgaagggg ctccttaagc gcaaggcctc gaactctccc acccacttcc aacccgaagc
     4801 tcgggatcaa gaatcacgta ctgcagccag gtggaagtaa ttcaaggcac gcaagggcca
     4861 taacccgtaa agaggccagg cccgcgggaa ccacacacgg cacttacctg tgttctggcg
     4921 gcaaacccgt tgcgaaaaag aacgttcacg gcgactactg cacttatata cggttctccc
     4981 ccaccctcgg gaaaaaggcg gagccagtac acgacatcac tttcccagtt taccccgcgc
     5041 caccttctct aggcaccggt tcaattgccg acccctcccc ccaacttctc ggggactgtg
     5101 ggcgatgtgc gctctgccca ctgacgggca ccggagccaa ttcccactcc tttcaagacc
     5161 tagaaggtcc attagctgca aagattcctc tctgtttaaa actttatcca tctttgcaaa
     5221 gctttttgca aaagcctagt caataatcaa tgtcaacgcg tatatctggc ccgtacatcg
     5281 cgaagcagcg caaaacgcct aaccctaagc agattcttca tgcaattgtc ggtcaagcct
     5341 tgccttgttg tagcttaaat tttgctcgcg cactactcag cgacctccaa cacacaagca
     5401 gggagcagat actggcttaa ctatgcggca tcagagcaga ttgtactgag agtgcaccat
     5461 aggggatcgg gagatctccc gatccgtcga cgtcaggtgg cacttttcgg ggaaatgtgc
     5521 gcggaacccc tatttgttta tttttctaaa tacattcaaa tatgtatccg ctcatgagac
     5581 aataaccctg ataaatgctt caataatatt gaaaaaggaa gagtatgagt attcaacatt
     5641 tccgtgtcgc ccttattccc ttttttgcgg cattttgcct tcctgttttt gctcacccag
     5701 aaacgctggt gaaagtaaaa gatgctgaag atcagttggg tgcacgagtg ggttacatcg
     5761 aactggatct caacagcggt aagatccttg agagttttcg ccccgaagaa cgttttccaa
     5821 tgatgagcac ttttaaagtt ctgctatgtg gcgcggtatt atcccgtatt gacgccgggc
     5881 aagagcaact cggtcgccgc atacactatt ctcagaatga cttggttgag tactcaccag
     5941 tcacagaaaa gcatcttacg gatggcatga cagtaagaga attatgcagt gctgccataa
     6001 ccatgagtga taacactgcg gccaacttac ttctgacaac gatcggagga ccgaaggagc
     6061 taaccgcttt tttgcacaac atgggggatc atgtaactcg ccttgatcgt tgggaaccgg
     6121 agctgaatga agccatacca aacgacgagc gtgacaccac gatgcctgta gcaatggcaa
     6181 caacgttgcg caaactatta actggcgaac tacttactct agcttcccgg caacaattaa
     6241 tagactggat ggaggcggat aaagttgcag gaccacttct gcgctcggcc cttccggctg
     6301 gctggtttat tgctgataaa tctggagccg gtgagcgtgg gtctcgcggt atcattgcag
     6361 cactggggcc agatggtaag ccctcccgta tcgtagttat ctacacgacg gggagtcagg
     6421 caactatgga tgaacgaaat agacagatcg ctgagatagg tgcctcactg attaagcatt
     6481 ggtaactgtc agaccaagtt tactcatata tactttagat tgatttaaaa cttcattttt
     6541 aatttaaaag gatctaggtg aagatccttt ttgataatct catgaccaaa atcccttaac
     6601 gtgagttttc gttccactga gcgtcagacc ccgtagaaaa gatcaaagga tcttcttgag
     6661 atcctttttt tctgcgcgta atctgctgct tgcaaacaaa aaaaccaccg ctaccagcgg
     6721 tggtttgttt gccggatcaa gagctaccaa ctctttttcc gaaggtaact ggcttcagca
     6781 gagcgcagat accaaatact gttcttctag tgtagccgta gttaggccac cacttcaaga
     6841 actctgtagc accgcctaca tacctcgctc tgctaatcct gttaccagtg gctgctgcca
     6901 gtggcgataa gtcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc
     6961 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     7021 ccgaactgag atacctacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     7081 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagcttc
     7141 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc
     7201 gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc agcaacgcgg
     7261 cctttttacg gttcctggcc ttttgctcac atgttctttc ctgcgttatc ccctgattct
     7321 gtggataacc gtattaccgc ctttgagtga gctgataccg ctcgccgcag ccgaacgacc
     7381 gagcgcagcg agtcagtgag cgaggaagcg gaagagcgcc caatacgcaa accgcctctc
     7441 cccgcgcgtt ggccgattca ttaatgcagc tggcacgaca ggtttcccga ctggaaagcg
     7501 ggcagtgagc gcaacgcaat taatgtgagt tagctcactc attaggcacc ccaggcttta
     7561 cactttatgc ttccggctcg tatgttgtgt ggaattgtga gcggataaca atttcacaca
     7621 ggaaacagct atgaccatga ttacgccaag ctctagctag aggtcgacgg tatacagaca
     7681 tgataagata cattgatgag tttggacaaa ccacaactag aatgcagtga aaaaaatgct
     7741 ttatttgtga aatttgtgat gctattgctt tatttgtaac cattataagc tgcaataaac
     7801 aagttggggt gggcgaagaa ctccagcatg agatccccgc gctggaggat catccagccg
     7861 gcgtcccgga aaacgattcc gaagcccaac ctttcataga aggcggcggt ggaatcgaaa
     7921 tctcgtagca cgtgtcagtc ctgctcctcg gccacgaagt gcttagccct cccacacata
     7981 accagagggc agcaattcac gaatcccaac tgccgtcggc tgtccatcac tgtccttcac
     8041 tatggctttg atcccaggat gcagatcgag aagcacctgt cggcaccgtc cgcaggggct
     8101 caagatgccc ctgttctcat ttccgatcgc gacgatacaa gtcaggttgc cagctgccgc
     8161 agcagcagca gtgcccagca ccacgagttc tgcacaaggt cccccagtaa aatgatatac
     8221 attgacacca gtgaagatgc ggccgtcgct agagagagct gcgctggcga cgctgtagtc
     8281 ttcagagatg gggatgctgt tgattgtagc cgttgctctt tcaatgaggg tggattcttc
     8341 ttgagacaaa ggcttggcca tggtttagtt cctcaccttg tcgtattata ctatgccgat
     8401 atactatgcc gatgattaat tgtcaacacg tgctgatcag atccgaaaat ggatatacaa
     8461 gctcccggga gctttttgca aaagcctagg cctccaaaaa agcctcctca ctacttctgg
     8521 aatagctcag aggcagaggc ggcctcggcc tctgcataaa t
//
