HhaI restriction site and cut
HhaI recognises GCGC and cuts G_CG^C, leaving a 2-base 3′ overhang (CG).
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.
At a glance
| Recognition site | GCGC |
|---|---|
| Site length | 4 bases |
| Cut | G_CG^C |
| Ends | a 2-base 3′ overhang (CG) |
| REBASE entry | HhaI 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) | 17 | 17 | 5, 108, 238, 259, 590, 655, 683, 716, 986, 1,053, 1,153, 1,327, 1,436, 1,829, 1,922, 2,259, 2,591 |
| pBR322 (J01749.1, 4,361 bp) | 31 | 31 | 103, 235, 263, 416, 437, 497, 551, 703, 778, 818, 949, 1,208, 1,359, 1,421, 1,457, 1,647, 1,730, 2,076, 2,179, 2,209, 2,350, 2,383, 2,653, 2,720, 2,820, 2,994, 3,103, 3,496, 3,589, 3,926, 4,258 |
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.