Fnu4HI restriction site and cut
Fnu4HI recognises GCNGC and cuts GC^N_GC, leaving a 1-base 5′ overhang (N).
In this notation, read on the top strand from five prime to three prime, ^ marks where the top strand is cut and _ where the bottom strand is cut. N stands for any base; Ns before or after the site are flanking bases, not part of it. The site uses IUPAC codes: N is any base.
At a glance
| Recognition site | GCNGC |
|---|---|
| Site length | 5 bases |
| Cut | GC^N_GC |
| Ends | a 1-base 5′ overhang (N) |
| REBASE entry | Fnu4HI on REBASE |
Sites in pUC19 and pBR322
| Vector | Sites | Cut under dam and dcm methylation | Cuts after base (top strand) |
|---|---|---|---|
| pUC19 (L09137.2, 2,686 bp) | 19 | 19 | 42, 151, 255, 328, 631, 712, 730, 733, 851, 1,006, 1,149, 1,214, 1,217, 1,423, 1,751, 2,090, 2,117, 2,212, 2,441 |
| pBR322 (J01749.1, 4,361 bp) | 42 | 42 | 227, 298, 301, 579, 582, 616, 723, 774, 939, 1,024, 1,107, 1,164, 1,209, 1,288, 1,407, 1,410, 1,417, 1,431, 1,560, 1,563, 1,686, 1,767, 2,064, 2,067, 2,113, 2,210, 2,263, 2,379, 2,397, 2,400, 2,518, 2,673, 2,816, 2,881, 2,884, 3,090, 3,418, 3,607, 3,757, 3,784, 3,879, 4,108 |
Counts are for the GenBank record named, as a circle, in that record's numbering. The third column counts the sites cut in DNA with dam and dcm methylation (the Drybench Plasmid default); any other site is blocked, or its outcome is not known. The positions list every recognition site, cut or not. 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.