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Sample files

Every file here is a synthetic example: invented sequences, nothing taken from a catalogue, a paper or a database. They are plain GenBank files; download them and open them in PlasmidPop with File ▸ Open, or drag them onto the window. Each tutorial names the files it needs and the order to open them in.

FileWhat it is
pLig-Vector.gbCircular 2,664 bp vector for the ligation exercises: synthetic promoter, MCS (EcoRI, PstI, BamHI, in that order), synthetic terminator, AmpR (a stand-in resistance gene, reverse strand), ori (a stand-in origin). EcoRI, PstI and BamHI cut it once each, all inside the MCS. Also the digest in Digest and PCR basics.
Insert-EcoRI-BamHI.gbLinear 819 bp: EcoRI site, the 783 bp ORF synthORF1 (ATG to stop), BamHI site, with a few bases of padding. No other EcoRI, BamHI or PstI site.
Insert-PstI-BamHI.gbThe same ORF with a PstI site where the EcoRI site was: the negative control.
Insert-EcoRI-EcoRI.gbThe same ORF with an EcoRI site at both ends, for single-enzyme cloning and dephosphorylation.
pGG-Expression.gbCircular 2,857 bp Golden Gate expression vector for Golden Gate: KanR (stand-in), ori, synthetic promoter, a lacZ-dropout between two BsaI sites, synthetic terminator. The slot asks for the overhangs AATG ... GCTT, the MoClo plant CDS pair.
GG-gene.gbLinear 702 bp synthGene, a plain ORF (ATG to stop) with no BsaI site and no Golden Gate ends, for Golden Gate: the app designs its primers.
pGG-Destination.gbCircular 2,647 bp Golden Gate destination vector: KanR (stand-in), ori, and a lacZ-dropout between two BsaI sites.
GG-prom.gbPart 1, 106 bp, synthetic promoter, BsaI overhangs GGAG ... AATG.
GG-cds.gbPart 2, 623 bp, synthCDS, a coding part without a stop, AATG ... TTCG.
GG-tag.gbPart 3, 55 bp, synthTag (a short linker and His tag ending in a stop codon), TTCG ... GCTT.
GG-term.gbPart 4, 96 bp, synthetic terminator, GCTT ... CGCT.
GG-broken-internal-BsaI.gbPart 3 with a third BsaI site inside it (54 bp).
GG-broken-duplicate-overhang.gbPart 3 whose right overhang is AATG, already taken by the promoter/CDS junction.
GG-warn-tag.gb, GG-warn-terminator.gbA replacement pair for parts 3 and 4 that joins on AATC, one base from AATG: assembles, with a warning.
MC-L1-Destination.gbCircular 1,572 bp level-1 destination vector for Modular cloning: AmpR (stand-in), ori, and a lacZ-dropout between two BsaI sites. Its backbone ends are CGCT and GGAG, which close a ring of MoClo plant positions.
MC-L0-Promoter-A.gb, MC-L0-Promoter-B.gbLevel-0 promoter parts (96 and 116 bp) for the MoClo position Promoter + 5′UTR, BsaI overhangs GGAG ... AATG. Alternatives to each other.
MC-L0-CDS-A.gb, MC-L0-CDS-B.gbLevel-0 coding parts (326 and 386 bp) for the position CDS, AATG ... GCTT: an open reading frame of 100 and 120 residues, ATG to stop.
MC-L0-Terminator.gbLevel-0 terminator part, 92 bp, for the position 3′UTR + terminator, GCTT ... CGCT.
MC-wrong-position.gbA 106 bp part cut for Yeast Toolkit Type 3 (TATG ... ATCC): it fits no MoClo plant position, so the panel does not place it.
GB-Vector.gbLinear 1,506 bp vector for Gibson, already linearised: synthetic terminator, KanR (stand-in, reverse strand), ori (stand-in), synthetic promoter. It starts with 26 bp that GB-Insert2 ends in and ends with 28 bp that GB-Insert1 starts with.
GB-Insert1.gbLinear 508 bp: the 28 bp vector overlap, synthDomainA (150 residues, ATG, no stop) and a 30 bp linker that GB-Insert2 starts with.
GB-Insert2.gbLinear 449 bp: the 30 bp linker, synthDomainB (130 residues, in frame with domain A, ending in a stop) and 26 bp of overlap with the vector.
GB-bad-Insert2.gbGB-Insert2 with one base of its 30 bp overlap changed (449 bp): the panel finds nothing that follows GB-Insert1.
pIF-Vector.gbCircular 1,446 bp vector for In-Fusion and NEBuilder: KanR (stand-in), ori, synthetic promoter, one EcoRV site (blunt), synthetic terminator.
IF-gene.gbLinear 603 bp synthProt, a plain ORF (ATG to stop, 200 residues) with no EcoRV site and no cloning ends, for In-Fusion and NEBuilder: the app designs its primers.
OE-Promoter.gbLinear 260 bp template for Overlap-extension PCR: a 160 bp synthetic promoter (bases 41 to 200) between flanking sequence.
OE-Gene.gbLinear 660 bp template: synthGene (bases 51 to 590), an ORF of 180 codons, ATG and no stop, between flanking sequence.
OE-Tag.gbLinear 169 bp template: synthTag (bases 41 to 109), a start codon, a linker, six histidines and a stop (23 codons), between flanking sequence.
OE-bad-Tag.gbOE-Tag with one extra base in front of its start codon (170 bp); synthTag starts on it with /codon_start=2: fused after the gene it is a base off the frame, and the panel says so.
GW-Insert.gbLinear 422 bp attB substrate for Gateway: attB1 (25 bp), synthGene (360 bp, ATG to stop, 120 codons) and attB2. The att sites are invented: a 15 base core with an arm on each side.
GW-pDONR.gbCircular 1,390 bp donor vector: attP1 and attP2 (55 bp each) around a ccdB stand-in, then KanR (reverse strand) and ori stand-ins. Invented att sites.
GW-pDEST.gbCircular 1,837 bp destination vector: promoter, attR1, ccdB and CmR stand-ins, attR2 (40 bp each site), terminator, AmpR (reverse strand) and ori. Invented att sites.
GW-bad-pDEST.gbGW-pDEST with attR3, a core nothing in the insert shares, where attR2 was (1,837 bp): the panel says the sites do not pair.
SDM-Template.gbCircular 1,241 bp plasmid for Site-directed mutagenesis: synthetic promoter, synthORF (100 codons and a stop, 139 to 441), synthetic terminator, one BamHI site, AT-rich spacer (90 bases of A and T only), AmpR and ori stand-ins. No EcoRV site.

Not here: the INS record (NM_000207). It is third party data, so you fetch it yourself in the app, from the NCBI box in the exercise; nothing in these pages contains it.

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