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pGEX-4T-1 digested with BsmAI
BsmAI recognises GTCTC and cuts circular pGEX-4T-1 (GenBank U13853.1, 4,969 bp) at 7 sites, so a complete digest gives 7 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
287
1,036
1,322
2
776
1,323
2,098
3
1,267
2,099
3,365
4
405
3,366
3,770
5
126
3,771
3,896
6
387
3,897
4,283
7
1,721
4,284
1,035
The fragments add up to 4,969 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
1,041
bottom strand
1,035
2
1,328
bottom strand
1,322
3
2,093
top strand
2,098
4
3,360
top strand
3,365
5
3,765
top strand
3,770
6
3,891
top strand
3,896
7
4,278
top strand
4,283
Positions are in the numbering of GenBank U13853.1. 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
pGEX-4T-1 (U13853.1) digested with BsmAI
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
BsmAI: GTCTC, cut GTCTCN^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/pgex-4t-1.1.json (GenBank U13853.1, SHA-256 7c27086ba934e96953ebd29bdcf2b5da67bcbcf2c0148bbb8dd4350aa8f59e38) 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.