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pGEM-3Z digested with FokI
FokI recognises GGATG and cuts circular pGEM-3Z (GenBank X65304.3, 2,743 bp) at 5 sites, so a complete digest gives 5 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
181
1,305
1,485
2
287
1,486
1,772
3
643
1,773
2,415
4
244
2,416
2,659
5
1,388
2,660
1,304
The fragments add up to 2,743 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Site reads on
Cuts after base (top strand)
1
1,318
bottom strand
1,304
2
1,499
bottom strand
1,485
3
1,786
bottom strand
1,772
4
2,402
top strand
2,415
5
2,646
top strand
2,659
Positions are in the numbering of GenBank X65304.3. A cut after base n leaves base n at the end of one fragment and the next base at the start of the next. A fragment that runs past the record's last base continues from its first. A vendor's map, or your own stock, may differ from this record.
The same question is open below in Drybench Plasmid. Change the enzymes, the host's methylation or the vector there; nothing you do here is saved unless you save it.
Reference dataset active
pGEM-3Z (X65304.3) digested with FokI
Opening what was sent…
Not medical advice. For research and education only, and not medical advice: this app designs restriction, Golden Gate and Gibson products from the sequences you supply; a designed product is not evidence that the reaction occurred, and nothing here predicts whether a reaction works, how well, or whether the product is expressed.
Ends
FokI: GGATG, cut GGATGNNNNNNNNN^NNNN_N, leaving a 4-base 5′ overhang whose bases are not fixed by the recognition site.
Methylation
Every one of these sites is cut in unmethylated DNA and in DNA from a dam and dcm methylating host, by the recorded dam and dcm sensitivities. Only dam and dcm are considered; CpG, EcoKI and other modifications are not modelled.
Source: McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1994;22:3640-3659 (doi 10.1093/nar/22.17.3640), Table I, read 6 October 2026.
The workspace draws a schematic gel of these fragments, not a prediction of where bands will run. Fragments under 100 bp are listed here but not drawn there, and fragments within 5 percent of each other are drawn as one band.
How this page was made
Computed when the site was built by the Drybench Plasmid engine, version 1.0.0, from /data/plasmid-map/examples/pgem-3z.1.json (GenBank X65304.3, SHA-256 4f560f61d69429fe294d5d5218159d1e5c69a7025ce66fc439c680ef7ffb6b9a) and enzyme table version 1, /data/plasmid-map/enzymes.8829d35c83.json (2026-10-06). Every cut position and fragment length on this page was compared with Biopython 1.88 (REBASE release 404, recorded 2026-11-07); a disagreement stops the build.