LOCUS       sequence-373218-        4642 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Shotgun Metagenomic Spike-in.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4642)
  AUTHORS   Zaramela LS, Tjuanta M, Moyne O, Neal M, Zengler K
  TITLE     synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification 
            of Shotgun Metagenomic Sequencing.
  JOURNAL   mSystems. 2022 Dec 20;7(6):e0044722. doi: 10.1128/msystems.00447-22.
            Epub 2022 Nov 1.
  PUBMED    36317886
REFERENCE   2  (bases 1 to 4642)
  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: "mSystems.";
            date: "2022-12-20"; volume: "7(6):e0044722. doi"; pages: " 
            10.1128/msystems.00447-22. Epub 2022 Nov 1"
COMMENT     Sequence Label: p236
FEATURES             Location/Qualifiers
     source          1..4642
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(29..51)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     151..170
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     364..386
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     378..395
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     379..395
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2421..2437)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2421..2437)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2434..2456)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2445..2461
                     /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(2469..2475,2476..2493,2494..2499))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    2514..2535
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(2652..2669)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2823..3411)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2903..2922)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3582..4373,4374..4442))
                     /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     4205..4224
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4443..4547)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     4615..4633
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
       61 cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
      121 ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc
      181 accatatgcg gtgtgaaata ccgcacagat gcgtaaggag aaaataccgc atcaggcgcc
      241 attcgccatt caggctgcgc aactgttggg aagggcgatc ggtgcgggcc tcttcgctat
      301 tacgccagct ggcgaaaggg ggatgtgctg caaggcgatt aagttgggta acgccagggt
      361 tttcccagtc acgacgttgt aaaacgacgg ccagtgaatt cgagctcggt acctcgcgaa
      421 tgcatctaga tctcgaggct tgaccgtatt tcggatgtac gcctagcgca cgattagtat
      481 gcgacagttt agggtaaccc tatcgataat cttgatctct cccagcaata gcaccagaca
      541 ctctaataaa gaaacacgtc cattctccag cttcgctaac cagtatatcc taaagttaat
      601 acggcatatt cctttaatta aatactcgtt atttattata atagatcctt gaacaactta
      661 gatactgtca taattatatt cattatgtaa ctttcggtga tcgatctgaa gtggacatgg
      721 taatatgctt actggtcaaa tatattacac attaaatcca gacaatcgct tattatgacc
      781 ttcgcagggt atgtgatact ttgaaagagc gtgctcagca ctggcttgtc accagccatt
      841 gattaatatc ttcagcatca ccttggacgg tttcagaatc gccgaataaa cctctaacgg
      901 caattctagc cctgcctact gtttagagag tgaaatgtct tacaagatca tcagcgtcgt
      961 aataagattc atcaagacag ttccgatagt ttcaaatcat caatccgggt tcctgttgca
     1021 cttgaaccta ttatgtctct taccctgggc ttcgttgctt ctgatattca aatcttacga
     1081 tgagcattta atgttagtat tagataaagt gaataggcat tattgccata tttcatccgg
     1141 agaaagacac gatgatgaac atctacaaag tcgggaaact ccgcaagaaa ctggactctt
     1201 actctttcta cgtaggcaat cacagtaagg atttattatt cacttattcc ttgcgattga
     1261 taaatgacgt ggtacgcctc agtgagtttg ctgcagtcaa ttatccataa cactactcct
     1321 tagacttgcg atctaacgtt tattgttatt aattattctt atgcggaccg tattaactgt
     1381 cttataggct ctatcggaac gctaatttct acgcgagtag ttattcacct ccaatgcact
     1441 agccttattt aagtccatgt cttcttcatc aaatacttag ggatatagtc ccggaattca
     1501 accaaatgtt ctagttattg tatttagtta aagctgttat gtttaagtta atgagattcc
     1561 tttaatggat actagctctg aacagtacca agttatgcta atcagccgaa tagatctgga
     1621 atacgcatgc ttattcatta attagattta ttacaacact tatagtcaat attagacact
     1681 tgcattataa ctgtgaacaa ggttggatta ggttgaatat gttccactca ttatagtatt
     1741 aagtaaggag tcgtgtattg ccctcttaaa gcaataataa ggatatttaa tttactctgg
     1801 cacacgtcca agagataaca agtgtttgat ctaattacgt aatgaggtca ttgaactact
     1861 tccaacttgg tgctgtctat aaagtggcta ctacaaaccg cggtgaattt ccggctttac
     1921 aatatcgtgg cacgcaacgc tgagcatttc tctacatttt cgtatcagtc aacttatcct
     1981 atattctatt gttatttatg catcgaaatt attcaatatg caatataata tgaaagatat
     2041 gtggtctaca tccgagcgcc gaatctaccg taatttgtta tcgaagtgaa actaataaga
     2101 tatcgttatg caattgcact ccacaatcca tgatcattat tgcaatgaat tgtaactatt
     2161 ccaaattaac tttaattaag caatatgttc catagacccc acagatagac ctttagcttg
     2221 ttatccacca tttatgaaat ctggcagcta gaggagtcta ctcagcacta ttggtatatt
     2281 aaagttcaga gattacttag cattctttaa atttgatagt ataaagtctg taattgagtc
     2341 cacatggtaa attcctaccc gggatcggat cccgggcccg tcgactgcag aggcctgcat
     2401 gcaagcttgg cgtaatcatg gtcatagctg tttcctgtgt gaaattgtta tccgctcaca
     2461 attccacaca acatacgagc cggaagcata aagtgtaaag cctggggtgc ctaatgagtg
     2521 agctaactca cattaattgc gttgcgctca ctgcccgctt tccagtcggg aaacctgtcg
     2581 tgccagctgc attaatgaat cggccaacgc gcggggagag gcggtttgcg tattgggcgc
     2641 tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta
     2701 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag
     2761 aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg
     2821 tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg
     2881 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg
     2941 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     3001 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc
     3061 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     3121 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact
     3181 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg
     3241 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt
     3301 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt
     3361 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct
     3421 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg
     3481 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt
     3541 aaatcaatct aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt
     3601 gaggcaccta tctcagcgat ctgtctattt cgttcatcca tagttgcctg actccccgtc
     3661 gtgtagataa ctacgatacg ggagggctta ccatctggcc ccagtgctgc aatgataccg
     3721 cgagacccac gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc
     3781 gagcgcagaa gtggtcctgc aactttatcc gcctccatcc agtctattaa ttgttgccgg
     3841 gaagctagag taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca
     3901 ggcatcgtgg tgtcacgctc gtcgtttggt atggcttcat tcagctccgg ttcccaacga
     3961 tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct
     4021 ccgatcgttg tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg
     4081 cataattctc ttactgtcat gccatccgta agatgctttt ctgtgactgg tgagtactca
     4141 accaagtcat tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata
     4201 cgggataata ccgcgccaca tagcagaact ttaaaagtgc tcatcattgg aaaacgttct
     4261 tcggggcgaa aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact
     4321 cgtgcaccca actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa
     4381 acaggaaggc aaaatgccgc aaaaaaggga ataagggcga cacggaaatg ttgaatactc
     4441 atactcttcc tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga
     4501 tacatatttg aatgtattta gaaaaataaa caaatagggg ttccgcgcac atttccccga
     4561 aaagtgccac ctgacgtcta agaaaccatt attatcatga cattaaccta taaaaatagg
     4621 cgtatcacga ggccctttcg tc
//
