LOCUS       sequence-461590-        7578 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  ProteinA-DddA11_NT for D.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 7578)
  AUTHORS   Chi WY, Yoon SH, Mekerishvili L, Ganesan S, Potenski C, Izzo F, 
            Landau D, Raimondi I
  TITLE     Single-cell mapping of regulatory DNA:Protein interactions.
  JOURNAL   bioRxiv [Preprint]. 2025 Jan 2:2024.12.31.630903. doi: 
            10.1101/2024.12.31.630903.
  PUBMED    39803441
REFERENCE   2  (bases 1 to 7578)
  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 Jan 2:2024.12.31.630903. doi: 
            10.1101/2024.12.31.630903."
COMMENT     Sequence Label: pTXB1-pA-DddA11_NT
FEATURES             Location/Qualifiers
     source          1..7578
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     126..148
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     CDS             complement(142..333)
                     /codon_start=1
                     /gene="rop"
                     /product="Rop protein, which maintains plasmids at low copy
                     number"
                     /label=rop
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
     CDS             complement(890..1972)
                     /codon_start=1
                     /gene="lacI"
                     /product="lac repressor"
                     /label=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)."
                     /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
                     NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
                     EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
                     EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
                     MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
                     YIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
                     ALADSLMQLARQVSRLESGQ"
     primer_bind     1934..1953
                     /label=LacI-R
                     /note="LacI, reverse primer"
     promoter        complement(1973..2050)
                     /gene="lacI"
                     /label=lacI promoter
     terminator      2203..2289
                     /gene="Escherichia coli rrnB"
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      2386..2472
                     /gene="Escherichia coli rrnB"
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      2569..2655
                     /gene="Escherichia coli rrnB"
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      2752..2838
                     /gene="Escherichia coli rrnB"
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     terminator      2935..3021
                     /gene="Escherichia coli rrnB"
                     /label=rrnB T1 terminator
                     /note="transcription terminator T1 from the E. coli rrnB 
                     gene"
     primer_bind     3156..3175
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        3156..3174
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     protein_bind    3175..3199
                     /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)."
     RBS             3214..3236
                     /note="efficient ribosome binding site from bacteriophage 
                     T7 gene 10 (Olins and Rangwala, 1989)"
     CDS             3249..3314
                     /codon_start=1
                     /product="three tandem FLAG(R) epitope tags, followed by an
                     enterokinase cleavage site"
                     /label=3xFLAG
                     /translation="DYKDHDGDYKDHDIDYKDDDDK"
     CDS             3333..3758
                     /codon_start=1
                     /product="immunoglobulin binding domains of Staphylocuccus 
                     aureus protein A"
                     /label=protein A
                     /translation="SLKDDPSQSANLLSEAKKLNESQAPKADNKFNKEQQNAFYEILHL
                     PNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAPKADNKFNKEQQNAFYEILHLP
                     NLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNDAQAPK"
     CDS             4167..4760
                     /codon_start=1
                     /gene="Mycobacterium xenopi gyrA"
                     /product="modified GyrA intein (Southworth et al., 1999)"
                     /label=Mxe GyrA intein
                     /note="N-terminal cleavage of this intein can be induced by
                     thiols."
                     /translation="CITGDALVALPEGESVRIADIVPGARPNSDNAIDLKVLDRHGNPV
                     LADRLFHSGEHPVYTVRTVEGLRVTGTANHPLLCLVDVAGVPTLLWKLIDEIKPGDYAV
                     IQRSAFSVDCAGFARGKPEFAPTTYTVGVPGLVRFLEAHHRDPDAQAIADELTDGRFYY
                     AKVASVTDAGVQPVYSLRVDTADHAFITNGFVSHA"
     CDS             4791..4946
                     /codon_start=1
                     /gene="Bacillus circulans chiA"
                     /product="chitin binding domain from chitinase A1 (Watanabe
                     et al., 1994)"
                     /label=CBD
                     /translation="TTNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNV
                     PALWQLQ"
     primer_bind     complement(5011..5029)
                     /label=T7 Term
                     /note="T7 terminator, reverse primer"
     terminator      5025..5072
                     /label=T7 terminator
                     /note="transcription terminator for bacteriophage T7 RNA 
                     polymerase"
     promoter        5132..5236
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5237..5305,5306..6097)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(5455..5474)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      complement(6139..6652)
                     /direction=LEFT
                     /label=M13 ori
                     /note="M13 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(6334..6355)
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     6546..6565
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     rep_origin      6763..7351
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     7252..7271
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     7505..7522
                     /label=L4440
                     /note="L4440 vector, forward primer"
     primer_bind     complement(7544..7563)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
ORIGIN
        1 atacactccg ctatcgctac gtgactgggt catggctgcg ccccgacacc cgccaacacc
       61 cgctgacgcg ccctgacggg cttgtctgct cccggcatcc gcttacagac aagctgtgac
      121 cgtctccggg agctgcatgt gtcagaggtt ttcaccgtca tcaccgaaac gcgcgaggca
      181 gctgcggtaa agctcatcag cgtggtcgtg cagcgattca cagatgtctg cctgttcatc
      241 cgcgtccagc tcgttgagtt tctccagaag cgttaatgtc tggcttctga taaagcgggc
      301 catgttaagg gcggtttttt cctgtttggt cactgatgcc tccgtgtaag ggggatttct
      361 gttcatgggg gtaatgatac cgatgaaacg agagaggatg ctcacgatac gggttactga
      421 tgatgaacat gcccggttac tggaacgttg tgagggtaaa caactggcgg tatggatgcg
      481 gcgggaccag agaaaaatca ctcagggtca atgccagccg aacgccagca agacgtagcc
      541 cagcgcgtcg gccgccatgc cggcgataat ggcctgcttc tcgccgaaac gtttggtggc
      601 gggaccagtg acgaaggctt gagcgagggc gtgcaagatt ccgaataccg caagcgacag
      661 gccgatcatc gtcgcgctcc agcgaaagcg gtcctcgccg aaaatgaccc agagcgctgc
      721 cggcacctgt cctacgagtt gcatgataaa gaagacagtc ataagtgcgg cgacgatagt
      781 catgccccgc gcccaccgga aggagctgac tgggttgaag gctctcaagg gcatcggtcg
      841 agatcccggt gcctaatgag tgagctaact tacattaatt gcgttgcgct cactgcccgc
      901 tttccagtcg ggaaacctgt cgtgccagct gcattaatga atcggccaac gcgcggggag
      961 aggcggtttg cgtattgggc gccagggtgg tttttctttt caccagtgag acgggcaaca
     1021 gctgattgcc cttcaccgcc tggccctgag agagttgcag caagcggtcc acgctggttt
     1081 gccccagcag gcgaaaatcc tgtttgatgg tggttaacgg cgggatataa catgagctgt
     1141 cttcggtatc gtcgtatccc actaccgaga tatccgcacc aacgcgcagc ccggactcgg
     1201 taatggcgcg cattgcgccc agcgccatct gatcgttggc aaccagcatc gcagtgggaa
     1261 cgatgccctc attcagcatt tgcatggttt gttgaaaacc ggacatggca ctccagtcgc
     1321 cttcccgttc cgctatcggc tgaatttgat tgcgagtgag atatttatgc cagccagcca
     1381 gacgcagacg cgccgagaca gaacttaatg ggcccgctaa cagcgcgatt tgctggtgac
     1441 ccaatgcgac cagatgctcc acgcccagtc gcgtaccgtc ttcatgggag aaaataatac
     1501 tgttgatggg tgtctggtca gagacatcaa gaaataacgc cggaacatta gtgcaggcag
     1561 cttccacagc aatggcatcc tggtcatcca gcggatagtt aatgatcagc ccactgacgc
     1621 gttgcgcgag aagattgtgc accgccgctt tacaggcttc gacgccgctt cgttctacca
     1681 tcgacaccac cacgctggca cccagttgat cggcgcgaga tttaatcgcc gcgacaattt
     1741 gcgacggcgc gtgcagggcc agactggagg tggcaacgcc aatcagcaac gactgtttgc
     1801 ccgccagttg ttgtgccacg cggttgggaa tgtaattcag ctccgccatc gccgcttcca
     1861 ctttttcccg cgttttcgca gaaacgtggc tggcctggtt caccacgcgg gaaacggtct
     1921 gataagagac accggcatac tctgcgacat cgtataacgt tactggtttc acattcacca
     1981 ccctgaattg actctcttcc gggcgctatc atgccatacc gcgaaaggtt ttgcgccatt
     2041 cgatggtgtc cgggatctcg acgctctccc ttatgcgact cctgcattag gaagcagccc
     2101 agtagtaggt tgaggccgtt gagcaccgcc gccgcaagga atggtgcatg ccggcatgcc
     2161 gccctttcgt cttcaagaat taattcccaa ttccccaggc atcaaataaa acgaaaggct
     2221 cagtcgaaag actgggcctt tcgttttatc tgttgtttgt cggtgaacgc tctcctgagt
     2281 aggacaaatc cgccgggagc ggatttgaac gttgcgaagc aacggcccgg agggtggcgg
     2341 gcaggacgcc cgccataaac tgccaggaat taattcccca ggcatcaaat aaaacgaaag
     2401 gctcagtcga aagactgggc ctttcgtttt atctgttgtt tgtcggtgaa cgctctcctg
     2461 agtaggacaa atccgccggg agcggatttg aacgttgcga agcaacggcc cggagggtgg
     2521 cgggcaggac gcccgccata aactgccagg aattaattcc ccaggcatca aataaaacga
     2581 aaggctcagt cgaaagactg ggcctttcgt tttatctgtt gtttgtcggt gaacgctctc
     2641 ctgagtagga caaatccgcc gggagcggat ttgaacgttg cgaagcaacg gcccggaggg
     2701 tggcgggcag gacgcccgcc ataaactgcc aggaattaat tccccaggca tcaaataaaa
     2761 cgaaaggctc agtcgaaaga ctgggccttt cgttttatct gttgtttgtc ggtgaacgct
     2821 ctcctgagta ggacaaatcc gccgggagcg gatttgaacg ttgcgaagca acggcccgga
     2881 gggtggcggg caggacgccc gccataaact gccaggaatt aattccccag gcatcaaata
     2941 aaacgaaagg ctcagtcgaa agactgggcc tttcgtttta tctgttgttt gtcggtgaac
     3001 gctctcctga gtaggacaaa tccgccggga gcggatttga acgttgcgaa gcaacggccc
     3061 ggagggtggc gggcaggacg cccgccataa actgccagga attggggatc ggaattaatt
     3121 cccggtttaa accggggatc tcgatcccgc gaaattaata cgactcacta taggggaatt
     3181 gtgagcggat aacaattccc ctctagaaat aattttgttt aactttaaga aggagatata
     3241 ccatgggtga ttacaaggat cacgatggcg attacaagga tcacgatatc gattacaagg
     3301 atgatgatga taagatgacc atgattacgc caagcttaaa agatgaccca agccaaagtg
     3361 ctaacctatt gtcagaagct aaaaagttaa atgaatctca agcaccgaaa gcggataaca
     3421 aattcaacaa agaacaacaa aatgctttct atgaaatctt acatttacct aacttaaacg
     3481 aagaacaacg caatggtttc atccaaagcc taaaagatga cccaagccaa agcgctaacc
     3541 ttttagcaga agctaaaaag ctaaatgatg ctcaagcacc aaaagctgac aacaaattca
     3601 acaaagaaca acaaaatgct ttctatgaaa ttttacattt acctaactta actgaagaac
     3661 aacgtaacgg cttcatccaa agccttaaag acgatccttc agtgagcaaa gaaattttag
     3721 cagaagctaa aaagctaaac gatgctcaag caccaaaaga tgacgataaa gaattcggtg
     3781 gcggtggctc tggcggtggt gggagtggag gtgggggatc aggaggaggc ggttcccata
     3841 tgggatctta cgctttagga ccgtatcaga tcagtgcccc tcaactgcca gcgtacaacg
     3901 gtcaaaccgt tggaacgttt tactatgtga atgatgcggg gggtcttgag agcaaagtat
     3961 ttattagcgg aggccccact ccctacccaa attatgtaag cgccggacac gttgagggtc
     4021 agtccgcact ttttatgcgc gacaacggaa tcagtgaggg gctggtgttc cataacaatc
     4081 caaaagggac ttgtggattc tgcgttaata tgattgaaac ccttctgcca gaaaacgcta
     4141 agatgacagt ggtgccccca gaagggtgca tcacgggaga tgcactagtt gccctacccg
     4201 agggcgagtc ggtacgcatc gccgacatcg tgccgggtgc gcggcccaac agtgacaacg
     4261 ccatcgacct gaaagtcctt gaccggcatg gcaatcccgt gctcgccgac cggctgttcc
     4321 actccggcga gcatccggtg tacacggtgc gtacggtcga aggtctgcgt gtgacgggca
     4381 ccgcgaacca cccgttgttg tgtttggtcg acgtcgccgg ggtgccgacc ctgctgtgga
     4441 agctgatcga cgaaatcaag ccgggcgatt acgcggtgat tcaacgcagc gcattcagcg
     4501 tcgactgtgc aggttttgcc cgcgggaaac ccgaatttgc gcccacaacc tacacagtcg
     4561 gcgtccctgg actggtgcgt ttcttggaag cacaccaccg agacccggac gcccaagcta
     4621 tcgccgacga gctgaccgac gggcggttct actacgcgaa agtcgccagt gtcaccgacg
     4681 ccggcgtgca gccggtgtat agccttcgtg tcgacacggc agaccacgcg tttatcacga
     4741 acgggttcgt cagccacgct actggcctca ccggtctgaa ctcaggcctc acgacaaatc
     4801 ctggtgtatc cgcttggcag gtcaacacag cttatactgc gggacaattg gtcacatata
     4861 acggcaagac gtataaatgt ttgcagcccc acacctcctt ggcaggatgg gaaccatcca
     4921 acgttcctgc cttgtggcag cttcaatgac tgcaggaagg ggatccggct gctaacaaag
     4981 cccgaaagga agctgagttg gctgctgcca ccgctgagca ataactagca taaccccttg
     5041 gggcctctaa acgggtcttg aggggttttt tgctgaaagg aggaactata tccggataac
     5101 tacgtcaggt ggcacttttc ggggaaatgt gcgcggaacc cctatttgtt tatttttcta
     5161 aatacattca aatatgtatc cgctcatgag acaataaccc tgataaatgc ttcaataata
     5221 ttgaaaaagg aagagtatga gtattcaaca tttccgtgtc gcccttattc ccttttttgc
     5281 ggcattttgc cttcctgttt ttgctcaccc agaaacgctg gtgaaagtaa aagatgctga
     5341 agatcagttg ggtgcacgag tgggttacat cgaactggat ctcaacagcg gtaagatcct
     5401 tgagagtttt cgccccgaag aacgtttccc aatgatgagc acttttaaag ttctgctatg
     5461 tggcgcggta ttatcccgtg ttgacgccgg gcaagagcaa ctcggtcgcc gcatacacta
     5521 ttctcagaat gacttggttg agtactcacc agtcacagaa aagcatctta cggatggcat
     5581 gacagtaaga gaattatgca gtgctgccat aaccatgagt gataacactg cggccaactt
     5641 acttctgaca acgatcggag gaccgaagga gctaaccgct tttttgcaca acatggggga
     5701 tcatgtaact cgccttgatc gttgggaacc ggagctgaat gaagccatac caaacgacga
     5761 gcgtgacacc acgatgcctg tagcaatggc aacaacgttg cgcaaactat taactggcga
     5821 actacttact ctagcttccc ggcaacaatt aatagactgg atggaggcgg ataaagttgc
     5881 aggaccactt ctgcgctcgg cccttccggc tggctggttt attgctgata aatctggagc
     5941 cggtgagcgt gggtctcgcg gtatcattgc agcactgggg ccagatggta agccctcccg
     6001 tatcgtagtt atctacacga cggggagtca ggcaactatg gatgaacgaa atagacagat
     6061 cgctgagata ggtgcctcac tgattaagca ttggtaactg tcagaccaag tttactcata
     6121 tatactttag attgatttac cccggttgat aatcagaaaa gccccaaaaa caggaagatt
     6181 gtataagcaa atatttaaat tgtaaacgtt aatattttgt taaaattcgc gttaaatttt
     6241 tgttaaatca gctcattttt taaccaatag gccgaaatcg gcaaaatccc ttataaatca
     6301 aaagaatagc ccgagatagg gttgagtgtt gttccagttt ggaacaagag tccactatta
     6361 aagaacgtgg actccaacgt caaagggcga aaaaccgtct atcagggcga tggcccacta
     6421 cgtgaaccat cacccaaatc aagttttttg gggtcgaggt gccgtaaagc actaaatcgg
     6481 aaccctaaag ggagcccccg atttagagct tgacggggaa agccggcgaa cgtggcgaga
     6541 aaggaaggga agaaagcgaa aggagcgggc gctagggcgc tggcaagtgt agcggtcacg
     6601 ctgcgcgtaa ccaccacacc cgccgcgctt aatgcgccgc tacagggcgc gtaaaaggat
     6661 ctaggtgaag atcctttttg ataatctcat gaccaaaatc ccttaacgtg agttttcgtt
     6721 ccactgagcg tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct
     6781 gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc
     6841 ggatcaagag ctaccaactc tttttccgaa ggtaactggc ttcagcagag cgcagatacc
     6901 aaatactgtc cttctagtgt agccgtagtt aggccaccac ttcaagaact ctgtagcacc
     6961 gcctacatac ctcgctctgc taatcctgtt accagtggct gctgccagtg gcgataagtc
     7021 gtgtcttacc gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg
     7081 aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata
     7141 cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta
     7201 tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc
     7261 ctggtatctt tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg
     7321 atgctcgtca ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt
     7381 cctggccttt tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt
     7441 ggataaccgt attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga
     7501 gcgcagcgag tcagtgagcg aggaagctat ggtgcactct cagtacaatc tgctctgatg
     7561 ccgcatagtt aagccagt
//
