Reference
Restriction enzyme reference
A searchable reference of common restriction enzymes: recognition site with the cut position marked, the overhang left behind, whether the enzyme is Type II or Type IIS, and which are everyday cloning workhorses. Filter by name or by recognition sequence.
| Enzyme | Recognition site | Overhang | Type | Common |
|---|---|---|---|---|
| AatII | GACGT^C | 3′ overhang | Type II | — |
| AflII | C^TTAAG | 5′ overhang | Type II | — |
| AgeI | A^CCGGT | 5′ overhang | Type II | — |
| AluI | AG^CT | blunt | Type II | yes |
| ApaI | GGGCC^C | 3′ overhang | Type II | — |
| AscI | GG^CGCGCC | 5′ overhang | Type II | — |
| AvrII | C^CTAGG | 5′ overhang | Type II | — |
| BamHI | G^GATCC | 5′ overhang | Type II | yes |
| BbsI | GAAGAC | 5′ overhang | Type IIS | yes |
| BclI | T^GATCA | 5′ overhang | Type II | — |
| BglII | A^GATCT | 5′ overhang | Type II | yes |
| BsaI | GGTCTC | 5′ overhang | Type IIS | yes |
| BsmBI | CGTCTC | 5′ overhang | Type IIS | yes |
| BspEI | T^CCGGA | 5′ overhang | Type II | — |
| BspQI | GCTCTTC | 5′ overhang | Type IIS | — |
| BsrGI | T^GTACA | 5′ overhang | Type II | — |
| BstBI | TT^CGAA | 5′ overhang | Type II | — |
| ClaI | AT^CGAT | 5′ overhang | Type II | — |
| DdeI | C^TNAG | 5′ overhang | Type II | — |
| DraI | TTT^AAA | blunt | Type II | — |
| EagI | C^GGCCG | 5′ overhang | Type II | — |
| EcoRI | G^AATTC | 5′ overhang | Type II | yes |
| EcoRV | GAT^ATC | blunt | Type II | yes |
| FseI | GGCCGG^CC | 3′ overhang | Type II | — |
| HaeIII | GG^CC | blunt | Type II | yes |
| HhaI | GCG^C | 3′ overhang | Type II | — |
| HindIII | A^AGCTT | 5′ overhang | Type II | yes |
| HinfI | G^ANTC | 5′ overhang | Type II | — |
| HpaI | GTT^AAC | blunt | Type II | — |
| HpaII | C^CGG | 5′ overhang | Type II | — |
| KpnI | GGTAC^C | 3′ overhang | Type II | yes |
| MboI | ^GATC | 5′ overhang | Type II | — |
| MfeI | C^AATTG | 5′ overhang | Type II | — |
| MluI | A^CGCGT | 5′ overhang | Type II | — |
| MspI | C^CGG | 5′ overhang | Type II | — |
| NarI | GG^CGCC | 5′ overhang | Type II | — |
| NcoI | C^CATGG | 5′ overhang | Type II | yes |
| NdeI | CA^TATG | 5′ overhang | Type II | yes |
| NheI | G^CTAGC | 5′ overhang | Type II | yes |
| NotI | GC^GGCCGC | 5′ overhang | Type II | yes |
| NruI | TCG^CGA | blunt | Type II | — |
| NsiI | ATGCA^T | 3′ overhang | Type II | — |
| PacI | TTAAT^TAA | 3′ overhang | Type II | — |
| PciI | A^CATGT | 5′ overhang | Type II | — |
| PmeI | GTTT^AAAC | blunt | Type II | — |
| PstI | CTGCA^G | 3′ overhang | Type II | yes |
| PvuII | CAG^CTG | blunt | Type II | yes |
| RsaI | GT^AC | blunt | Type II | — |
| SacI | GAGCT^C | 3′ overhang | Type II | yes |
| SacII | CCGC^GG | 3′ overhang | Type II | — |
| SalI | G^TCGAC | 5′ overhang | Type II | yes |
| SapI | GCTCTTC | 5′ overhang | Type IIS | — |
| Sau3AI | ^GATC | 5′ overhang | Type II | yes |
| SbfI | CCTGCA^GG | 3′ overhang | Type II | — |
| ScaI | AGT^ACT | blunt | Type II | — |
| SmaI | CCC^GGG | blunt | Type II | yes |
| SnaBI | TAC^GTA | blunt | Type II | — |
| SpeI | A^CTAGT | 5′ overhang | Type II | yes |
| SphI | GCATG^C | 3′ overhang | Type II | — |
| StuI | AGG^CCT | blunt | Type II | — |
| SwaI | ATTT^AAAT | blunt | Type II | — |
| TaqI | T^CGA | 5′ overhang | Type II | — |
| XbaI | T^CTAGA | 5′ overhang | Type II | yes |
| XhoI | C^TCGAG | 5′ overhang | Type II | yes |
| XmaI | C^CCGGG | 5′ overhang | Type II | — |
| No enzyme matches that search. | ||||
65 enzymes listed
The caret marks the top-strand cut for Type II enzymes. Type IIS enzymes cut a fixed distance outside their recognition site, so no caret is shown; use the restriction sites tool to place their exact cut on a sequence.
A quick reference for cloning design. To find where these enzymes cut a specific sequence, or to scan for unique and non-cutting sites, use the restriction sites tool. Recognition sites are written 5′ to 3′ on the top strand.
Frequently asked
How do I find where an enzyme cuts my sequence?
This page is a lookup table, not a scanner. Paste your sequence into the restriction sites tool to map cut positions, count fragments and find unique or non-cutting enzymes.
Why is there no cut mark on some enzymes?
Type IIS enzymes recognise one sequence but cut a defined distance away from it, so a caret inside the site would be misleading. The restriction sites tool places their cut correctly on a real sequence.
Do two enzymes with the same site cut identically?
Isoschizomers share a recognition sequence but may cut at different positions or leave different ends, and they differ in star activity and buffer needs. Check the supplier’s data for the exact enzyme you will use.