LOCUS       sequence-373235-        4724 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 4724)
  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 4724)
  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: p136
FEATURES             Location/Qualifiers
     source          1..4724
                     /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"
     CDS             complement(1775..1786)
                     /codon_start=1
                     /product="Factor Xa recognition and cleavage site"
                     /label=Factor Xa site
                     /translation="IEGR"
     primer_bind     complement(2503..2519)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(2503..2519)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(2516..2538)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    2527..2543
                     /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(2551..2557,2558..2575,2576..2581))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    2596..2617
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(2734..2751)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2905..3493)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2985..3004)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(3664..4455,4456..4524))
                     /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     4287..4306
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(4525..4629)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     4697..4715
                     /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 tgtttaaact tgtacgtctt tccgagtatg ccaacattaa tagtatagcg
      481 caattcagat agcagcatta aggtaataaa gcaaggaaac gcgccaccga ttagagattt
      541 catgctcttt acaaagtcag tggaattctt atattagaca cggtatttgt acatattgcc
      601 taaatatagt atgcaaattg gcgtgaatat tcataaattc ccataagttg tgacgtgatt
      661 gattattcga attaagatat tatcattccg ttgttcgaac ttaatctaat taccacctta
      721 gatagtgtta ttattgtaga tctatctgag ggagaatata aatacgggaa ttaaaccctt
      781 aacagtgcag ttgagttctc ctaagcttag acaaatggat caacaccttg tcgcaaattg
      841 acatagtccg ttattggtta tggaataaac cttatgccta cctcggctgc attaaatcgc
      901 aatttaatag atacgactgt atctatttac cttacggcat cacactacct agacttcagt
      961 atatgccagc atttactaaa tagctaaata ataaggttac taataagatc cgattaggcc
     1021 tataaatccg cgggagtcga atagtatacc atatattaca tgagatttga gaggaaggca
     1081 ttgcctgatc tagtctataa gagagaatat ccagcagttg aaattattat catcgtttga
     1141 ccctccgctc cttacgggct aagtagattc gcagaataga taatttagaa ggaataccga
     1201 cgactataca taaccatgga gaatctaaat attacaaatt gacatacgtc ttctcagcac
     1261 caggttccat tataagttta cctgctaaat tattcttgaa gcgaacagac tccaggaaat
     1321 aagaatatga tggtggatcc attactataa ttctgtccag aataatcggc acgctaattg
     1381 cgagtataat ataatcatga gttataacgc aaggattgac ttagtaatta taatcactgt
     1441 taagaatgtt ggcaggtata agaagtgcaa cgtaacctct cgtatcgaac actccagtta
     1501 ttatatgacc actgaagtcg aacggaagtt gaagtcagcc ctctacattt cttcaattag
     1561 atgtggccaa tcgtggttaa tagtctaagt ctgttctggc agatctaact aatatagaca
     1621 tagcctgctc gtctcgtatg accacaggga ttatatccta cgtcattgct gacgttaata
     1681 agatcaggcg attacataat aatatgaacg tatttgtact atttggtgat ttaaagtcct
     1741 caacccgcgt gacgtattat atctaactaa taaatcgacc ttcaatgtgg cgatctactt
     1801 catatcttcc caagactaag tgcccgtcat agcatgcttc gtttaaagca tttatttcga
     1861 ttatctttaa tgcccgttaa atattatata attaggactg ccatacggta ggccgtattg
     1921 caactttcac ttcactatac catatcatta tttagggcta gacgttcatg tcactaataa
     1981 gggtgcttaa ctcggcccat tatctcttct taagagagga cgtaccttgg cctaaacaat
     2041 agatccttta tgcacctggt acactacatc acgtgacaac aagactggac gtcagtatga
     2101 tgctaatacc gcttgtaaat ctattagatg cgtaaatgaa tgtcgtgata tctaatccaa
     2161 gcccgtgagt tggtcacttc attgtcgccc ggctcttctg gattaaacaa caaatttaac
     2221 ggatacaatg ctatgtggtt tacgccacta ttgatatcct tgtgcaatta tgcttgatca
     2281 atggtattaa cgagaagtta taatctaatt tacttcttta tgagttccac tatcgatacg
     2341 tgatctcaca atgcctaata tacgatcacg aatcaagtgg tagaaaggga tggtcgtata
     2401 gacaaatgaa cccgtccaac ctcaacgtaa atatggtttc tcgagatcgg atcccgggcc
     2461 cgtcgactgc agaggcctgc atgcaagctt ggcgtaatca tggtcatagc tgtttcctgt
     2521 gtgaaattgt tatccgctca caattccaca caacatacga gccggaagca taaagtgtaa
     2581 agcctggggt gcctaatgag tgagctaact cacattaatt gcgttgcgct cactgcccgc
     2641 tttccagtcg ggaaacctgt cgtgccagct gcattaatga atcggccaac gcgcggggag
     2701 aggcggtttg cgtattgggc gctcttccgc ttcctcgctc actgactcgc tgcgctcggt
     2761 cgttcggctg cggcgagcgg tatcagctca ctcaaaggcg gtaatacggt tatccacaga
     2821 atcaggggat aacgcaggaa agaacatgtg agcaaaaggc cagcaaaagg ccaggaaccg
     2881 taaaaaggcc gcgttgctgg cgtttttcca taggctccgc ccccctgacg agcatcacaa
     2941 aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat accaggcgtt
     3001 tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta ccggatacct
     3061 gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct gtaggtatct
     3121 cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc
     3181 cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa gacacgactt
     3241 atcgccactg gcagcagcca ctggtaacag gattagcaga gcgaggtatg taggcggtgc
     3301 tacagagttc ttgaagtggt ggcctaacta cggctacact agaagaacag tatttggtat
     3361 ctgcgctctg ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa
     3421 acaaaccacc gctggtagcg gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa
     3481 aaaaggatct caagaagatc ctttgatctt ttctacgggg tctgacgctc agtggaacga
     3541 aaactcacgt taagggattt tggtcatgag attatcaaaa aggatcttca cctagatcct
     3601 tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga
     3661 cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc
     3721 catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg
     3781 ccccagtgct gcaatgatac cgcgagaccc acgctcaccg gctccagatt tatcagcaat
     3841 aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat
     3901 ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg
     3961 caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc
     4021 attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa
     4081 agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc
     4141 actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt
     4201 ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag
     4261 ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa ctttaaaagt
     4321 gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag
     4381 atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac
     4441 cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc
     4501 gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca
     4561 gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg
     4621 ggttccgcgc acatttcccc gaaaagtgcc acctgacgtc taagaaacca ttattatcat
     4681 gacattaacc tataaaaata ggcgtatcac gaggcccttt cgtc
//
