LOCUS       sequence-487863-        6782 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Proximity-labeling proteomics negative control.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 6782)
  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 6782)
  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"; journalName: "bioRxiv 
            [Preprint]. 2025 Mar 21:2025.02.26.640373. doi: 
            10.1101/2025.02.26.640373."
COMMENT     Sequence Label: pEF myc-TurboID
FEATURES             Location/Qualifiers
     source          1..6782
                     /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"
     promoter        351..1529
                     /label=EF-1-alpha promoter
                     /note="strong constitutive promoter for human elongation 
                     factor EF-1-alpha"
     intron          582..1520
                     /label=EF-1-alpha intron A
                     /note="intron upstream of the start codon of human 
                     EF-1-alpha"
     primer_bind     1477..1497
                     /label=EF1a-F
                     /note="Human elongation factor-1a promoter, forward primer"
     primer_bind     1546..1565
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        1546..1564
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     CDS             1686..1715
                     /codon_start=1
                     /product="Myc (human c-Myc proto-oncogene) epitope tag"
                     /label=Myc
                     /translation="EQKLISEEDL"
     CDS             1734..2690
                     /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             2697..2723
                     /codon_start=1
                     /product="nuclear export signal from the HIV Rev protein 
                     (Fischer et al., 1995)"
                     /label=NES
                     /translation="LPPLERLTL"
     primer_bind     complement(2749..2766)
                     /label=BGH-rev
                     /note="Bovine growth hormone terminator, reverse primer. 
                     Also called BGH reverse"
     polyA_signal    2755..2979
                     /label=bGH poly(A) signal
                     /note="bovine growth hormone polyadenylation signal"
     rep_origin      3025..3453
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(3112..3131)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     3322..3343
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(3462..3482)
                     /label=pBABE 3'
                     /note="SV40 enhancer, reverse primer for pBABE vectors"
     promoter        3467..3796
                     /label=SV40 promoter
                     /note="SV40 enhancer and early promoter"
     rep_origin      3647..3782
                     /label=SV40 ori
                     /note="SV40 origin of replication"
     primer_bind     3709..3728
                     /label=SV40pro-F
                     /note="SV40 promoter/origin, forward primer"
     promoter        3844..3891
                     /label=EM7 promoter
                     /note="synthetic bacterial promoter "
     CDS             3910..4308
                     /codon_start=1
                     /gene="Aspergillus terreus BSD"
                     /product="blasticidin S deaminase"
                     /label=BSD
                     /note="confers resistance to blasticidin"
                     /translation="MAKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTG
                     VNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGI
                     KAIVKDSDGQPTAVGIRELLPSGYVWEG"
     polyA_signal    4466..4587
                     /label=SV40 poly(A) signal
                     /note="SV40 polyadenylation signal"
     primer_bind     complement(4503..4522)
                     /label=SV40pA-R
                     /note="SV40 polyA, reverse primer"
     primer_bind     4557..4576
                     /label=EBV-rev
                     /note="SV40 polyA terminator, reverse primer"
     primer_bind     complement(4636..4652)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(4636..4652)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(4649..4671)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    4660..4676
                     /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(4684..4690,4691..4708,4709..4714))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4729..4750
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(4867..4884)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(5027..5615)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(5107..5126)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(5786..6577,6578..6646))
                     /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"
     promoter        complement(6647..6751)
                     /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 taggcttttg caaaaagctt tgcaaagatg gataaagttt taaacagaga
      301 ggaatctttg cagctaatgg accttctagg tcttgaaagg agtgggaatt ggctccggtg
      361 cccgtcagtg ggcagagcgc acatcgccca cagtccccga gaagttgggg ggaggggtcg
      421 gcaattgaac cggtgcctag agaaggtggc gcggggtaaa ctgggaaagt gatgtcgtgt
      481 actggctccg cctttttccc gagggtgggg gagaaccgta tataagtgca gtagtcgccg
      541 tgaacgttct ttttcgcaac gggtttgccg ccagaacaca ggtaagtgcc gtgtgtggtt
      601 cccgcgggcc tggcctcttt acgggttatg gcccttgcgt gccttgaatt acttccacct
      661 ggctgcagta cgtgattctt gatcccgagc ttcgggttgg aagtgggtgg gagagttcga
      721 ggccttgcgc ttaaggagcc ccttcgcctc gtgcttgagt tgaggcctgg cctgggcgct
      781 ggggccgccg cgtgcgaatc tggtggcacc ttcgcgcctg tctcgctgct ttcgataagt
      841 ctctagccat ttaaaatttt tgatgacctg ctgcgacgct ttttttctgg caagatagtc
      901 ttgtaaatgc gggccaagat ctgcacactg gtatttcggt ttttggggcc gcgggcggcg
      961 acggggcccg tgcgtcccag cgcacatgtt cggcgaggcg gggcctgcga gcgcggccac
     1021 cgagaatcgg acgggggtag tctcaagctg gccggcctgc tctggtgcct ggcctcgcgc
     1081 cgccgtgtat cgccccgccc tgggcggcaa ggctggcccg gtcggcacca gttgcgtgag
     1141 cggaaagatg gccgcttccc ggccctgctg cagggagctc aaaatggagg acgcggcgct
     1201 cgggagagcg ggcgggtgag tcacccacac aaaggaaaag ggcctttccg tcctcagccg
     1261 tcgcttcatg tgactccacg gagtaccggg cgccgtccag gcacctcgat tagttctcga
     1321 gcttttggag tacgtcgtct ttaggttggg gggaggggtt ttatgcgatg gagtttcccc
     1381 acactgagtg ggtggagact gaagttaggc cagcttggca cttgatgtaa ttctccttgg
     1441 aatttgccct ttttgagttt ggatcttggt tcattctcaa gcctcagaca gtggttcaaa
     1501 gtttttttct tccatttcag gtgtcgtgag gaattagctt ggtactaata cgactcacta
     1561 tagggagacc caagctggct aggtaagctt ggtaccgagc tcggatccac tagtccagtg
     1621 tggtggaatt ctgcagatat ccagcacagt ggcggccgct cgagtctaga gggcccttca
     1681 ccatggaaca aaaactcatc tcagaagagg atctgggagg gcagtctggg cagaaagaca
     1741 atactgtgcc tctgaagctg atcgctctcc tggctaatgg cgagttccat agtggcgaac
     1801 agctgggaga aaccctgggc atgtccaggg ccgctatcaa caagcacatt cagactctgc
     1861 gcgactgggg cgtggacgtg ttcaccgtgc ccggaaaggg ctactctctg cccgagccta
     1921 tcccgctgct gaacgctaaa cagattctgg gacagctgga cggcgggagc gtggcagtcc
     1981 tgcctgtggt cgactccacc aatcagtacc tgctggatcg aatcggcgag ctgaagagtg
     2041 gggatgcttg cattgcagaa tatcagcagg cagggagagg aagcagaggg aggaaatggt
     2101 tctctccttt tggagctaac ctgtacctga gtatgttttg gcgcctgaag cggggaccag
     2161 cagcaatcgg cctgggcccg gtcatcggaa ttgtcatggc agaagcgctg cgaaagctgg
     2221 gagcagacaa ggtgcgagtc aaatggccca atgacctgta tctgcaggat agaaagctgg
     2281 caggcatcct ggtggagctg gccggaataa caggcgatgc tgcacagatc gtcattggcg
     2341 ccgggattaa cgtggctatg aggcgcgtgg aggaaagcgt ggtcaatcag ggctggatca
     2401 cactgcagga agcagggatt aacctggaca ggaatactct ggccgctacg ctgatccgag
     2461 agctgcgggc agccctggaa ctgttcgagc aggaaggcct ggctccatat ctgccacggt
     2521 gggagaagct ggataacttc atcaatagac ccgtgaagct gatcattggg gacaaagaga
     2581 ttttcgggat tagccggggg attgataaac agggagccct gctgctggaa caggacggag
     2641 ttatcaaacc ctggatgggc ggagaaatca gtctgcggtc tgccgaaaag ctgcagctgc
     2701 ctcccctgga gcgcctgacc ctggactaag tttaaacccg ctgatcagcc tcgactgtgc
     2761 cttctagttg ccagccatct gttgtttgcc cctcccccgt gccttccttg accctggaag
     2821 gtgccactcc cactgtcctt tcctaataaa atgaggaaat tgcatcgcat tgtctgagta
     2881 ggtgtcattc tattctgggg ggtggggtgg ggcaggacag caagggggag gattgggaag
     2941 acaatagcag gcatgctggg gatgcggtgg gctctatggc ttctgaggcg gaaagaacca
     3001 gctggggctc tagggggtat ccccacgcgc cctgtagcgg cgcattaagc gcggcgggtg
     3061 tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc gctcctttcg
     3121 ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct ctaaatcggg
     3181 ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa aaacttgatt
     3241 agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc cctttgacgt
     3301 tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca ctcaacccta
     3361 tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat tggttaaaaa
     3421 atgagctgat ttaacaaaaa tttaacgcga attaattctg tggaatgtgt gtcagttagg
     3481 gtgtggaaag tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta
     3541 gtcagcaacc aggtgtggaa agtccccagg ctccccagca ggcagaagta tgcaaagcat
     3601 gcatctcaat tagtcagcaa ccatagtccc gcccctaact ccgcccatcc cgcccctaac
     3661 tccgcccagt tccgcccatt ctccgcccca tggctgacta atttttttta tttatgcaga
     3721 ggccgaggcc gcctctgcct ctgagctatt ccagaagtag tgaggaggct tttttggagg
     3781 cctaggcttt tgcaaaaagc tcccgggagc ttgtatatcc attttcggat ctgatcagca
     3841 cgtgttgaca attaatcatc ggcatagtat atcggcatag tataatacga caaggtgagg
     3901 aactaaacca tggccaagcc tttgtctcaa gaagaatcca ccctcattga aagagcaacg
     3961 gctacaatca acagcatccc catctctgaa gactacagcg tcgccagcgc agctctctct
     4021 agcgacggcc gcatcttcac tggtgtcaat gtatatcatt ttactggggg accttgtgca
     4081 gaactcgtgg tgctgggcac tgctgctgct gcggcagctg gcaacctgac ttgtatcgtc
     4141 gcgatcggaa atgagaacag gggcatcttg agcccctgcg gacggtgccg acaggtgctt
     4201 ctcgatctgc atcctgggat caaagccata gtgaaggaca gtgatggaca gccgacggca
     4261 gttgggattc gtgaattgct gccctctggt tatgtgtggg agggctaagc acttcgtggc
     4321 cgaggagcag gactgacacg tgctacgaga tttcgattcc accgccgcct tctatgaaag
     4381 gttgggcttc ggaatcgttt tccgggacgc cggctggatg atcctccagc gcggggatct
     4441 catgctggag ttcttcgccc accccaactt gtttattgca gcttataatg gttacaaata
     4501 aagcaatagc atcacaaatt tcacaaataa agcatttttt tcactgcatt ctagttgtgg
     4561 tttgtccaaa ctcatcaatg tatcttatca tgtctgtata ccgtcgacct ctagctagag
     4621 cttggcgtaa tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc tcacaattcc
     4681 acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat gagtgagcta
     4741 actcacatta attgcgttgc gctcactgcc cgctttccag tcgggaaacc tgtcgtgcca
     4801 gctgcattaa tgaatcggcc aacgcgcggg gagaggcggt ttgcgtattg ggcgctcttc
     4861 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc
     4921 tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat
     4981 gtgagcaaaa ggccaggaac cgtaaaaagg ccgcgttgct ggcgtttttc cataggctcc
     5041 gcccccctga cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag
     5101 gactataaag ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga
     5161 ccctgccgct taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc
     5221 atagctcacg ctgtaggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg
     5281 tgcacgaacc ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt
     5341 ccaacccggt aagacacgac ttatcgccac tggcagcagc cactggtaac aggattagca
     5401 gagcgaggta tgtaggcggt gctacagagt tcttgaagtg gtggcctaac tacggctaca
     5461 ctagaagaac agtatttggt atctgcgctc tgctgaagcc agttaccttc ggaaaaagag
     5521 ttggtagctc ttgatccggc aaacaaacca ccgctggtag cggtggtttt tttgtttgca
     5581 agcagcagat tacgcgcaga aaaaaaggat ctcaagaaga tcctttgatc ttttctacgg
     5641 ggtctgacgc tcagtggaac gaaaactcac gttaagggat tttggtcatg agattatcaa
     5701 aaaggatctt cacctagatc cttttaaatt aaaaatgaag ttttaaatca atctaaagta
     5761 tatatgagta aacttggtct gacagttacc aatgcttaat cagtgaggca cctatctcag
     5821 cgatctgtct atttcgttca tccatagttg cctgactccc cgtcgtgtag ataactacga
     5881 tacgggaggg cttaccatct ggccccagtg ctgcaatgat accgcgagac ccacgctcac
     5941 cggctccaga tttatcagca ataaaccagc cagccggaag ggccgagcgc agaagtggtc
     6001 ctgcaacttt atccgcctcc atccagtcta ttaattgttg ccgggaagct agagtaagta
     6061 gttcgccagt taatagtttg cgcaacgttg ttgccattgc tacaggcatc gtggtgtcac
     6121 gctcgtcgtt tggtatggct tcattcagct ccggttccca acgatcaagg cgagttacat
     6181 gatcccccat gttgtgcaaa aaagcggtta gctccttcgg tcctccgatc gttgtcagaa
     6241 gtaagttggc cgcagtgtta tcactcatgg ttatggcagc actgcataat tctcttactg
     6301 tcatgccatc cgtaagatgc ttttctgtga ctggtgagta ctcaaccaag tcattctgag
     6361 aatagtgtat gcggcgaccg agttgctctt gcccggcgtc aatacgggat aataccgcgc
     6421 cacatagcag aactttaaaa gtgctcatca ttggaaaacg ttcttcgggg cgaaaactct
     6481 caaggatctt accgctgttg agatccagtt cgatgtaacc cactcgtgca cccaactgat
     6541 cttcagcatc ttttactttc accagcgttt ctgggtgagc aaaaacagga aggcaaaatg
     6601 ccgcaaaaaa gggaataagg gcgacacgga aatgttgaat actcatactc ttcctttttc
     6661 aatattattg aagcatttat cagggttatt gtctcatgag cggatacata tttgaatgta
     6721 tttagaaaaa taaacaaata ggggttccgc gcacatttcc ccgaaaagtg ccacctgacg
     6781 tc
//
