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REBASE - restriction enzymes and methylases
Introduction
Acknowledgements
References
REBASE - restriction enzymes and methylases
ABSTRACT
INTRODUCTION
The restriction enzyme database, REBASE, is a collection of information about restriction enzymes and methylases. Since the last description of the contents of REBASE (1), 79 new entries have been added. These include two Type II enzymes with new specificities: BseMII which recognizes the sequence CTSAG (2), and HaeIV, which recognizes the sequence GAYNNNNNRTC (3). Among the 2900 restriction enzymes now known, there are 19 fully characterized Type I specificities, 212 different Type II specificities and four different Type III specificities. Table 1 contains a listing of all prototype restriction enzymes (Types I, II and III), together with their commercially available isoschizomers and neoschizomers. Homing endonucleases (4) are also listed in REBASE and seven of the 37 known are commercially available (see Table 2). REBASE currently stores 4696 published references, with abstracts, and 486 unpublished observations.
Table 1
Type II restriction enzymes
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| AatII | GACGT[darr]C | ADEFKLMNOPRS | ||
| AccI | GT[darr]MKAC | 5(6) | ABDEGJKLMNOPQRS | |
| (AceIII) | CAGCTC(7/11) | |||
| AciI | CCGC(-3/-1) | N | ||
| AclI | AA[darr]CGTT | IN | ||
| Psp1406I | AA[darr]CGTT | DFKM | ||
| AcyI | GR[darr]CGYC | JM | ||
| BbiII | GR[darr]CGYC | K | ||
| BsaHI | GR[darr]CGYC | N | ||
| BstACI | GR[darr]CGYC | I | ||
| Hin1I | GR[darr]CGYC | EFO | ||
| Hsp92I | GR[darr]CGYC | R | ||
| Msp17I | GR[darr]CGYC | D | ||
| AflII | C[darr]TTAAG | ABJKNO | ||
| BfrI | C[darr]TTAAG | MO | ||
| BspTI | C[darr]TTAAG | DF | ||
| Bst98I | C[darr]TTAAG | R | ||
| MspCI | C[darr]TTAAG | C | ||
| Vha464I | C[darr]TTAAG | I | ||
| AflIII | A[darr]CRYGT | ABMN | ||
| AgeI | A[darr]CCGGT | ?(5) | JNR | |
| AsiAI | A[darr]CCGGT | I | ||
| PinAI | A[darr]CCGGT | BM | ||
| (AhaIII) | DraI | TTT[darr]AAA | ABDEFGIJKLMNOPQRS | |
| AluI | AG[darr]CT | 3(5) | ABCDEFGHIJKLMNOPQRST | |
| AlwNI | CAGNNN[darr]CTG | ABN | ||
| ApaI | GGGCC[darr]C | 4(5) | ABEGIJKLMNOPQRS | |
| Bsp120I | G[darr]GGCCC | DFN | ||
| PspOMI | G[darr]GGCCC | I | ||
| (ApaBI) | BstAPI | GCANNNN[darr]NTGC | IN | |
| ApaLI | G[darr]TGCAC | ?(5) | ADEKN | |
| Alw44I | G[darr]TGCAC | FJMORS | ||
| VneI | G[darr]TGCAC | I | ||
| ApoI | R[darr]AATTY | ?(6) | N | |
| AcsI | R[darr]AATTY | DIM | ||
| AscI | GG[darr]CGCGCC | ?(5) | N | |
| (AsuI) | AspS9I | G[darr]GNCC | I | |
| BsiZI | G[darr]GNCC | T | ||
| Cfr13I | G[darr]GNCC | 4(5) | DFKO | |
| Sau96I | G[darr]GNCC | 4(5) | AJLMNOR | |
| (FmuI) | GGNC[darr]C | |||
| (AsuII) | Bpu14I | TT[darr]CGAA | I | |
| BsiCI | TT[darr]CGAA | T | ||
| Bsp119I | TT[darr]CGAA | DF | ||
| BstBI | TT[darr]CGAA | N | ||
| PsyI | GACN[darr]NNGTC | |||
| CbiI | TT[darr]CGAA | J | ||
| Csp45I | TT[darr]CGAA | OR | ||
| LspI | TT[darr]CGAA | L |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| NspV | TT[darr]CGAA | ABJKO | ||
| SfuI | TT[darr]CGAA | M | ||
| AvaI | C[darr]YCGRG | ?(4) | ABEGJKLMNOPQRS | |
| Ama87I | C[darr]YCGRG | DI | ||
| BcoI | C[darr]YCGRG | AT | ||
| BsoBI | C[darr]YCGRG | ?(4) | N | |
| Eco88I | C[darr]YCGRG | F | ||
| (Nli387/7I) | CYCGR[darr]G | |||
| AvaII | G[darr]GWCC | ?(5) | ABEGJKMNPQRS | |
| Bme18I | G[darr]GWCC | I | ||
| Eco47I | G[darr]GWCC | FO | ||
| HgiEI | G[darr]GWCC | ?(5) | D | |
| SinI | G[darr]GWCC | 4(5) | LR | |
| (VpaK11AI) | [darr]GGWCC | |||
| (AvaIII) | EcoT22I | ATGCA[darr]T | AKO | |
| Mph1103I | ATGCA[darr]T | F | ||
| NsiI | ATGCA[darr]T | BDEHJLMNRS | ||
| Zsp2I | ATGCA[darr]T | I | ||
| Ppu10I | A[darr]TGCAT | DN | ||
| (BfrBI) | ATG[darr]CAT | |||
| AvrII | C[darr]CTAGG | N | ||
| BlnI | C[darr]CTAGG | AKMS | ||
| BspA2I | C[darr]CTAGG | I | ||
| (BaeI)e | (10/15)ACNNNNGTAYC(12/7) | 1(6),-4(6) | ||
| BalI | TGG[darr]CCA | 4(4) | AJKR | |
| MlsI | TGG[darr]CCA | F | ||
| MluNI | TGG[darr]CCA | MS | ||
| MscI | TGG[darr]CCA | BDNOS | ||
| BamHI | G[darr]GATCC | 5(4) | ABCDEFGHIJKLMNOPQRST | |
| BbvI | GCAGC(8/12) | 2(5),-2(5) | N | |
| Bst71I | GCAGC(8/12) | R | ||
| (BbvII) | BbsI | GAAGAC(2/6) | N | |
| BpiI | GAAGAC(2/6) | DF | ||
| BpuAI | GAAGAC(2/6) | M | ||
| (BccI) | CCATC | |||
| (Bce83I) | CTTGAG(16/14) | |||
| (BcefI) | ACGGC(12/13) | |||
| BcgI5 | (10/12)GCANNNNNNTCG(12/10) | 3(6),-3(6) | N | |
| BciVI | GTATCC(6/5) | N | ||
| BclI | T[darr]GATCA | BCDEFGJLMNOPRS | ||
| BsiQI | T[darr]GATCA | T | ||
| FbaI | T[darr]GATCA | AK | ||
| Ksp22I | T[darr]GATCA | I | ||
| (BetI) | BsaWI | W[darr]CCGGW | N | |
| (BfiI) | ACTGGG(4/5) | |||
| BglI | GCCNNNN[darr]NGGC | ?(4) | ABCDEFGHIJKLMNOPQRST | |
| BglII | A[darr]GATCT | 5(4) | ABCDEFGHIJKLMNOPQRST | |
| (BinI) | AclWI | GGATC(4/5) | I | |
| AlwI | GGATC(4/5) | N | ||
| (BmgI) | GKGCCC |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| (BplI) | GAGNNNNNCTC | |||
| Bpu10I | CCTNAGC(-5/-2) | F | ||
| BsaAI | YAC[darr]GTR | N | ||
| BstBAI | YAC[darr]GTR | I | ||
| BsaBI | GATNN[darr]NNATC | N | ||
| Bse8I | GATNN[darr]NNATC | I | ||
| Bsh1365I | GATNN[darr]NNATC | DF | ||
| BsiBI | GATNN[darr]NNATC | T | ||
| BsrBRI | GATNN[darr]NNATC | R | ||
| MamI | GATNN[darr]NNATC | ?(6) | M | |
| (BsaXI) | ACNNNNNCTCC | |||
| (BsbI) | CAACAC | |||
| (BscGI) | CCCGT | |||
| (BseMII) | CTSAG | |||
| BsePI | G[darr]CGCGC | I | ||
| BssHII | G[darr]CGCGC | ?(5) | ABDEJKLMNOPQRS | |
| PauI | G[darr]CGCGC | F | ||
| BseRI | GAGGAG(10/8) | N | ||
| BsgI | GTGCAG(16/14) | N | ||
| (BsiI) | BssSI | CACGAG(-5/-1) | N | |
| Bst2BI | CACGAG(-5/-1) | DI | ||
| BsiYI | CCNNNNN[darr]NNGG | MT | ||
| Bsc4I | CCNNNNN[darr]NNGG | I | ||
| BseLI | CCNNNNN[darr]NNGG | F | ||
| BslI | CCNNNNN[darr]NNGG | N | ||
| BsmI | GAATGC(1/-1) | ABDEJLMNOS | ||
| BsaMI | GAATGC(1/-1) | R | ||
| BscCI | GAATGC(1/-1) | T | ||
| Mva1269I | GAATGC(1/-1) | F | ||
| BsmAI | GTCTC(1/5) | N | ||
| Alw26I | GTCTC(1/5) | 3(5),-4(6) | DFR | |
| (Bsp24I)e | (8/13)GACNNNNNNTGG(12/7) | |||
| Bsp1407I | T[darr]GTACA | DFK | ||
| AauI | T[darr]GTACA | I | ||
| BsrGI | T[darr]GTACA | N | ||
| SspBI | T[darr]GTACA | M | ||
| (BspGI) | CTGGAC | |||
| BspHI | T[darr]CATGA | AN | ||
| PagI | T[darr]CATGA | F | ||
| RcaI | T[darr]CATGA | BM | ||
| BspLU11I | A[darr]CATGT | M | ||
| BspMI | ACCTGC(4/8) | N | ||
| (BspMII) | AccIII | T[darr]CCGGA | EJKQR | |
| BseAI | T[darr]CCGGA | CM | ||
| BsiMI | T[darr]CCGGA | AT | ||
| Bsp13I | T[darr]CCGGA | I | ||
| BspEI | T[darr]CCGGA | N | ||
| Kpn2I | T[darr]CCGGA | BDF | ||
| MroI | T[darr]CCGGA | MO | ||
| BsrI | ACTGG(1/-1) | N |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| Bse1I | ACTGG(1/-1) | I | ||
| BseNI | ACTGG(1/-1) | DF | ||
| BsrSI | ACTGG(1/-1) | R | ||
| BsrBI | CCGCTC(-3/-3) | N | ||
| AccBSI | CCGCTC(-3/-3) | DI | ||
| MbiI | CCGCTC(-3/-3) | F | ||
| BsrDI | GCAATG(2/0) | N | ||
| Bse3DI | GCAATG(2/0) | I | ||
| BstEII | G[darr]GTNACC | BDGHJLMNORS | ||
| BstPI | G[darr]GTNACC | K | ||
| Eco91I | G[darr]GTNACC | F | ||
| EcoO65I | G[darr]GTNACC | AK | ||
| PspEI | G[darr]GTNACC | I | ||
| BstXI | CCANNNNN[darr]NTGG | ABDEFGHJKLMNOQRS | ||
| Cac8I | GCN[darr]NGC | N | ||
| (CauII) | AsuC2I | CC[darr]SGG | I | |
| BcnI | CC[darr]SGG | 2(4) | ADFK | |
| NciI | CC[darr]SGG | BEJLMNORST | ||
| (EcoHI) | [darr]CCSGG | |||
| CfrI | Y[darr]GGCCR | 4(5) | F | |
| EaeI | Y[darr]GGCCR | 4(5) | ADKLMN | |
| Cfr10I | R[darr]CCGGY | 2(5) | ADFKMO | |
| Bse118I | R[darr]CCGGY | I | ||
| BsrFI | R[darr]CCGGY | N | ||
| BssAI | R[darr]CCGGY | C | ||
| (CjeI)5 | (8/14)CCANNNNNNGT(15/9) | |||
| (CjePI)5 | (7/13)CCANNNNNNNTC(14/8) | |||
| ClaI | AT[darr]CGAT | 5(6) | ABHKMNPRST | |
| BanIII | AT[darr]CGAT | O | ||
| Bsa29I | AT[darr]CGAT | I | ||
| BscI | AT[darr]CGAT | L | ||
| BseCI | AT[darr]CGAT | 5(6) | C | |
| BsiXI | AT[darr]CGAT | T | ||
| Bsp106I | AT[darr]CGAT | 5(6) | E | |
| BspDI | AT[darr]CGAT | N | ||
| BspXI | AT[darr]CGAT | G | ||
| Bsu15I | AT[darr]CGAT | 5(6) | DF | |
| CviJI | RG[darr]CY | 3(5) | Q | |
| (CviRI) | TG[darr]CA | 4(6) | ||
| DdeI | C[darr]TNAG | 1(5) | ABEGLMNORS | |
| BstDEI | C[darr]TNAG | DI | ||
| DpnI* | Gm6A[darr]TC | ABELMNRS | ||
| DraII | RG[darr]GNCCY | AGMS | ||
| EcoO109I | RG[darr]GNCCY | ABDEFJKLN | ||
| (PssI) | RGGNC[darr]CY | |||
| DraIII | CACNNN[darr]GTG | AEGMNS | ||
| AdeI | CACNNN[darr]GTG | F | ||
| DrdI | GACNNNN[darr]NNGTC | N | ||
| DseDI | GACNNNN[darr]NNGTC | I | ||
| (DrdII) | GAACCA |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| DsaI | C[darr]CRYGG | M | ||
| BstDSI | C[darr]CRYGG | DI | ||
| Eam1105I | GACNNN[darr]NNGTC | DFK | ||
| AhdI | GACNNN[darr]NNGTC | N | ||
| AspEI | GACNNN[darr]NNGTC | M | ||
| EclHKI | GACNNN[darr]NNGTC | R | ||
| NruGI | GACNNN[darr]NNGTC | I | ||
| (EciI) | TCCGCC | |||
| Eco31I | GGTCTC(1/5) | 4(5),-4(6) | DF | |
| BsaI | GGTCTC(1/5) | N | ||
| Eco47III | AGC[darr]GCT | BDEFLMNORS | ||
| AfeI | AGC[darr]GCT | I | ||
| Aor51HI | AGC[darr]GCT | AK | ||
| Eco57I | CTGAAG(16/14) | 5(6),-5(6) | DFN | |
| EcoNI | CCTNN[darr]NNNAGG | AN | ||
| XagI | CCTNN[darr]NNNAGG | F | ||
| EcoRI | G[darr]AATTC | 3(6) | ABCDEFGHIJKLMNOPQRST | |
| EcoRIIf | [darr]CCWGG | 2(5) | BEJMOS | |
| + | BsiLI | CC[darr]WGG | T | |
| + | Bst2UI | CC[darr]WGG | I | |
| + | BstNI | CC[darr]WGG | 2(4) | CEN |
| + | BstOI | CC[darr]WGG | R | |
| + | MvaI | CC[darr]WGG | 2(4) | ADFKMOS |
| EcoRV | GAT[darr]ATC | 2(6) | ABCDEGHIJKLMNOPQRST | |
| Eco32I | GAT[darr]ATC | F | ||
| (EspI) | BlpI | GC[darr]TNAGC | N | |
| Bpu1102I | GC[darr]TNAGC | BDEFK | ||
| Bsp1720I | GC[darr]TNAGC | I | ||
| CelII | GC[darr]TNAGC | ALM | ||
| Esp3I | CGTCTC(1/5) | 4(5),-4(6) | DF | |
| BsmBI | CGTCTC(1/5) | N | ||
| FauI | CCCGC(4/6) | I | ||
| FinI | GGGAC | |||
| BsmFI | GGGAC(10/14) | N | ||
| Fnu4HI | GC[darr]NGC | N | ||
| Fsp4HI | GC[darr]NGC | I | ||
| ItaI | GC[darr]NGC | M | ||
| (FnuDII) | AccII | CG[darr]CG | AJKQ | |
| Bsh1236I | CG[darr]CG | DEF | ||
| BstUI | CG[darr]CG | N | ||
| MvnI | CG[darr]CG | M | ||
| ThaI | CG[darr]CG | B | ||
| (SelI) | [darr]CGCG | |||
| FokI | GGATG(9/13) | 3(6),-2(6) | ADGIJKLMNR | |
| BseGI | GGATG(2/0) | F | ||
| BstF5I | GGATG(2/0) | 3(6) | IN | |
| (StsI) | GGATG(10/14) | 3(6),-2(6) | ||
| FseI | GGCCGG[darr]CC | ?(5) | AKN | |
| (GdiII) | CGGCCR(-5/-1) | |||
| GsuI | CTGGAG(16/14) | DF |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| BpmI | CTGGAG(16/14) | N | ||
| (HaeI) | WGG[darr]CCW | |||
| HaeII | RGCGC[darr]Y | ABDEGJKLMNORS | ||
| Bsp143II | RGCGC[darr]Y | F | ||
| BstH2I | RGCGC[darr]Y | I | ||
| (LpnI) | RGC[darr]GCY | |||
| HaeIII | GG[darr]CC | 3(5) | ABCDGHIJKLMNOPQRST | |
| BshI | GG[darr]CC | T | ||
| BsuRI | GG[darr]CC | 3(5) | FI | |
| PalI | GG[darr]CC | E | ||
| (HaeIV) | GAYNNNNNRTC | 2(6) | ||
| HgaI | GACGC(5/10) | 3(5),-2(5) | AN | |
| (HgiAI) | Alw21I | GWGCW[darr]C | DF | |
| AspHI | GWGCW[darr]C | M | ||
| Bbv12I | GWGCW[darr]C | I | ||
| BsiHKAI | GWGCW[darr]C | N | ||
| (HgiCI) | AccB1I | G[darr]GYRCC | I | |
| BanI | G[darr]GYRCC | ?(5) | AEMNORS | |
| BshNI | G[darr]GYRCC | F | ||
| Eco64I | G[darr]GYRCC | DF | ||
| (HgiEII) | ACCNNNNNNGGT | |||
| (HgiJII) | BanII | GRGCY[darr]C | 4(5) | ABKLMNOQRS |
| Eco24I | GRGCY[darr]C | DF | ||
| EcoT38I | GRGCY[darr]C | J | ||
| FriOI | GRGCY[darr]C | I | ||
| HhaI | GCG[darr]C | 2(5) | ABGJKNOPR | |
| AspLEI | GCG[darr]C | I | ||
| CfoI | GCG[darr]C | BLMRS | ||
| Hin6I | G[darr]CGC | DF | ||
| HinP1I | G[darr]CGC | N | ||
| HspAI | G[darr]CGC | I | ||
| (Hin4I) | GABNNNNNVTC | |||
| HindII | GTY[darr]RAC | 5(6) | MS | |
| HincII | GTY[darr]RAC | 5(6) | ABCDEFGHJKLNOPQR | |
| HindIII | A[darr]AGCTT | 1(6) | ABCDEFGHIJKLMNOPQRST | |
| HinfI | G[darr]ANTC | ABDEFGHIJKLMNOPQRST | ||
| HpaI | GTT[darr]AAC | 5(6) | ABDEGHJKLMNOPQRST | |
| BstHPI | GTT[darr]AAC | I | ||
| KspAI | GTT[darr]AAC | F | ||
| HpaII | C[darr]CGG | 2(5) | BDEFGILMNOPQRS | |
| BsiSI | C[darr]CGG | C | ||
| HapII | C[darr]CGG | 2(5) | AK | |
| Hin2I | C[darr]CGG | F | ||
| MspI | C[darr]CGG | 1(5) | ABDEFGHIJKLMNOPQRS | |
| HphI | GGTGA(8/7) | 5(6),-2(5) | AFN | |
| AsuHPI | GGTGA(8/7) | I | ||
| KpnI | GGTAC[darr]C | 4(6) | ABCDEFGHIJKLMNOPQRST | |
| Acc65I | G[darr]GTACC | DFINR | ||
| Asp718I | G[darr]GTACC | M | ||
| Ksp632I | CTCTTC(1/4) | M |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| Bsu6I | CTCTTC(1/4) | I | ||
| Eam1104I | CTCTTC(1/4) | DEF | ||
| EarI | CTCTTC(1/4) | N | ||
| MaeI | C[darr]TAG | M | ||
| BfaI | C[darr]TAG | N | ||
| MaeII | A[darr]CGT | M | ||
| TaiI | ACGT[darr] | FN | ||
| TscI | ACGT[darr] | L | ||
| MaeIII | [darr]GTNAC | M | ||
| MboIg | [darr]GATC | 2(6) | ABCEFGKLNQRT | |
| BscFI | [darr]GATC | T | ||
| + | Bsp143I | [darr]GATC | DF | |
| DpnII | [darr]GATC | 2(6) | N | |
| Kzo9I | [darr]GATC | I | ||
| NdeII | [darr]GATC | BDGJMS | ||
| + | Sau3AI | [darr]GATC | 4(5) | ABEGHJKLMNOPQRS |
| + | BspKT6I | GAT[darr]C | 2(6) | |
| ChaI | GATC[darr] | |||
| MboII | GAAGA(8/7) | 5(6) | ABDFGJKNOQR | |
| (McrI) | BsaOI | CGRY[darr]CG | R | |
| Bsh1285I | CGRY[darr]CG | DF | ||
| BsiEI | CGRY[darr]CG | N | ||
| BstMCI | CGRY[darr]CG | I | ||
| MfeI | C[darr]AATTG | N | ||
| MunI | C[darr]AATTG | 3(6) | BDEFKMS | |
| MluI | A[darr]CGCGT | ABDEFGIJKLMNOPQRS | ||
| (MmeI) | TCCRAC(20/18) | |||
| MnlI | CCTC(7/6) | AEFNQ | ||
| MseI | T[darr]TAA | BN | ||
| Tru1I | T[darr]TAA | F | ||
| Tru9I | T[darr]TAA | DILMR | ||
| MslI | CAYNN[darr]NNRTG | N | ||
| (MstI) | Acc16I | TGC[darr]GCA | DI | |
| AviII | TGC[darr]GCA | M | ||
| FspI | TGC[darr]GCA | ABJKNOS | ||
| NsbI | TGC[darr]GCA | F | ||
| MwoI | GCNNNNN[darr]NNGC | ?(5) | N | |
| NaeI | GCC[darr]GGC | ADEKLMNORS | ||
| MroNI | G[darr]CCGGC | I | ||
| NgoAIV | G[darr]CCGGC | B | ||
| NgoMI | G[darr]CCGGC | 2(5) | NR | |
| NarI | GG[darr]CGCC | BEJMNOPRS | ||
| BbeI | GGCGC[darr]C | AK | ||
| EgeI | GGC[darr]GCC | I | ||
| EheI | GGC[darr]GCC | ADFNO | ||
| KasI | G[darr]GCGCC | N | ||
| Mly113I | GG[darr]CGCC | I | ||
| NcoI | C[darr]CATGG | ?(4) | ABCDEFGHJKLMNOPQRST | |
| Bsp19I | C[darr]CATGG | I | ||
| NdeI | CA[darr]TATG | ABDEFGJKLMNPRS |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| FauNDI | CA[darr]TATG | DI | ||
| NheI | G[darr]CTAGC | ABDEFGJKLMNOPRS | ||
| AsuNHI | G[darr]CTAGC | I | ||
| (AceII) | GCTAG[darr]C | |||
| NlaIII | CATG[darr] | 2(6) | ANO | |
| Hsp92II | CATG[darr] | R | ||
| (CviAII) | C[darr]ATG | 2(6) | ||
| NlaIV | GGN[darr]NCC | N | ||
| BscBI | GGN[darr]NCC | T | ||
| BspLI | GGN[darr]NCC | F | ||
| PspN4I | GGN[darr]NCC | I | ||
| NotI | GC[darr]GGCCGC | ?(4) | ABCDEFGHJKLMNOPQRST | |
| CciNI | GC[darr]GGCCGC | I | ||
| NruI | TCG[darr]CGA | ABCDEGIJKLMNOQRST | ||
| Bsp68I | TCG[darr]CGA | F | ||
| NspI | RCATG[darr]Y | ABKM | ||
| BstNSI | RCATG[darr]Y | DI | ||
| NspBII | CMG[darr]CKG | A | ||
| MspA1I | CMG[darr]CKG | INR | ||
| PacI | TTAAT[darr]TAA | NO | ||
| Pfl1108I | TCGTAG | |||
| PflMI | CCANNNN[darr]NTGG | ANS | ||
| AccB7I | CCANNNN[darr]NTGG | IR | ||
| Esp1396I | CCANNNN[darr]NTGG | F | ||
| Van91I | CCANNNN[darr]NTGG | DFKM | ||
| PleI | GAGTC(4/5) | N | ||
| (MlyI) | GACTC(5/5) | |||
| PmaCI | CAC[darr]GTG | AK | ||
| BbrPI | CAC[darr]GTG | MO | ||
| Eco72I | CAC[darr]GTG | DEFR | ||
| PmlI | CAC[darr]GTG | N | ||
| PmeI | GTTT[darr]AAAC | N | ||
| PpuMI | RG[darr]GWCCY | ANO | ||
| Psp5II | RG[darr]GWCCY | BDF | ||
| PspPPI | RG[darr]GWCCY | I | ||
| PshAI | GACNN[darr]NNGTC | AKN | ||
| PstI | CTGCA[darr]G | 5(6) | ABCDEFGHIJKLMNOPQRST | |
| PvuI | CGAT[darr]CG | ABDEFGKLMNOPQRS | ||
| BspCI | CGAT[darr]CG | E | ||
| Ple19I | CGAT[darr]CG | I | ||
| PvuII | CAG[darr]CTG | 4(4) | ABCDEFGHIJKLMNOPQRST | |
| (RleAI) | CCCACA(12/9) | |||
| RsaI | GT[darr]AC | ABCDEFGIJLMNOPQRST | ||
| AfaI | GT[darr]AC | K | ||
| Csp6I | G[darr]TAC | DFN | ||
| RsrII | CG[darr]GWCCG | BMN | ||
| CpoI | CG[darr]GWCCG | ADFK | ||
| CspI | CG[darr]GWCCG | EOR | ||
| SacI | GAGCT[darr]C | 5(?) | ACEFGHJKLMNOPQRST | |
| Ecl136II | GAG[darr]CTC | DFN |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| EcoICRI | GAG[darr]CTC | R | ||
| Psp124BI | GAGCT[darr]C | DI | ||
| SstI | GAGCT[darr]C | BC | ||
| SacII | CCGC[darr]GG | ACEGHJKLNOPQRT | ||
| Cfr42I | CCGC[darr]GG | DF | ||
| KspI | CCGC[darr]GG | MS | ||
| Sfr303I | CCGC[darr]GG | I | ||
| SstII | CCGC[darr]GG | B | ||
| (Mlu113I) | CC[darr]GCGG | |||
| SalI | G[darr]TCGAC | 5(6) | ABCDEFGHIJKLMNOPQRST | |
| SanDI | GG[darr]GWCCC | E | ||
| SapI | GCTCTTC(1/4) | N | ||
| (SauI) | AocI | CC[darr]TNAGG | M | |
| AxyI | CC[darr]TNAGG | J | ||
| Bse21I | CC[darr]TNAGG | I | ||
| Bsu36I | CC[darr]TNAGG | ENR | ||
| CvnI | CC[darr]TNAGG | B | ||
| Eco81I | CC[darr]TNAGG | ADFKO | ||
| ScaI | AGT[darr]ACT | ABCDEFGJKLMNOPQRS | ||
| Acc113I | AGT[darr]ACT | I | ||
| Eco255I | AGT[darr]ACT | F | ||
| ScrFI | CC[darr]NGG | ?(5) | DJMNOS | |
| BssKI | [darr]CCNGG | N | ||
| MspR9I | CC[darr]NGG | I | ||
| SduI | GDGCH[darr]C | F | ||
| BmyI | GDGCH[darr]C | M | ||
| Bsp1286I | GDGCH[darr]C | ADJKNR | ||
| (SecI) | BsaJI | C[darr]CNNGG | N | |
| BseDI | C[darr]CNNGG | DF | ||
| SexAI | A[darr]CCWGGT | M | ||
| SfaNI | GCATC(5/9) | IN | ||
| (BscAI) | GCATC(4/6) | |||
| (SfeI) | BfmI | C[darr]TRYAG | F | |
| BstSFI | C[darr]TRYAG | DI | ||
| SfcI | C[darr]TRYAG | N | ||
| SfiI | GGCCNNNN[darr]NGGCC | ?(4) | ABCDEGIJKLMNOPQRST | |
| SgfI | GCGAT[darr]CGC | R | ||
| SgrAI | CR[darr]CCGGYG | M | ||
| (SimI) | GGGTC(-3/0) | |||
| SmaI | CCC[darr]GGG | 2(4) | ABCDEFGHIJKLMNOPQRST | |
| Cfr9I | C[darr]CCGGG | 2(4) | FO | |
| PspAI | C[darr]CCGGG | E | ||
| XmaI | C[darr]CCGGG | ?(4) | ADINPR | |
| XmaCI | C[darr]CCGGG | M | ||
| SmlI | C[darr]TYRAG | N | ||
| (SnaI) | BssNAI | GTA[darr]TAC | I | |
| Bst1107I | GTA[darr]TAC | DFKM | ||
| BstZ17I | GTA[darr]TAC | N | ||
| SnaBI | TAC[darr]GTA | ACEKLMNR | ||
| BstSNI | TAC[darr]GTA | DI |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| Eco105I | TAC[darr]GTA | FO | ||
| SpeI | A[darr]CTAGT | ABDEHJKLMNOPQRST | ||
| AclNI | A[darr]CTAGT | I | ||
| BcuI | A[darr]CTAGT | F | ||
| SphI | GCATG[darr]C | ABCDEGHIJKLMNOPQRST | ||
| BbuI | GCATG[darr]C | R | ||
| PaeI | GCATG[darr]C | F | ||
| SplI | C[darr]GTACG | AK | ||
| BsiWI | C[darr]GTACG | MNO | ||
| Pfl23II | C[darr]GTACG | DF | ||
| PspLI | C[darr]GTACG | I | ||
| SunI | C[darr]GTACG | B | ||
| SrfI | GCCC[darr]GGGC | EO | ||
| Sse8387I | CCTGCA[darr]GG | AK | ||
| SbfI | CCTGCA[darr]GG | DIN | ||
| SdaI | CCTGCA[darr]GG | F | ||
| (Sse8647I) | AG[darr]GWCCT | |||
| SspI | AAT[darr]ATT | ?(6) | ABCDEFIJKLMNOPQRS | |
| StuI | AGG[darr]CCT | ABEJKLMNPQRST | ||
| AatI | AGG[darr]CCT | O | ||
| Eco147I | AGG[darr]CCT | DF | ||
| Pme55I | AGG[darr]CCT | I | ||
| SseBI | AGG[darr]CCT | C | ||
| StyI | C[darr]CWWGG | BCEJMNRS | ||
| BssT1I | C[darr]CWWGG | I | ||
| Eco130I | C[darr]CWWGG | DF | ||
| EcoT14I | C[darr]CWWGG | AK | ||
| ErhI | C[darr]CWWGG | I | ||
| SwaI | ATTT[darr]AAAT | MS | ||
| SmiI | ATTT[darr]AAAT | DFI | ||
| TaqI | T[darr]CGA | 4(6) | ABCDEFGIJLMNOPQRST | |
| TthHB8I | T[darr]CGA | 4(6) | AK | |
| (TaqII)h | CACCCA(11/9) | |||
| (TaqII)h | GACCGA(11/9) | |||
| TatI | W[darr]GTACW | F | ||
| (TauI) | GCSGC | |||
| TfiI | G[darr]AWTC | N | ||
| TseI | G[darr]CWGC | N | ||
| Tsp45I | [darr]GTSAC | N | ||
| (Tsp4CI) | Bst4CI | ACN[darr]GT | I | |
| TspEI | [darr]AATT | LO | ||
| Sse9I | [darr]AATT | 2(6) | DI | |
| Tsp509I | [darr]AATT | N | ||
| TspRI | CASTGNN[darr] | N | ||
| Tth111I | GACN[darr]NNGTC | ADIKNQR | ||
| AspI | GACN[darr]NNGTC | MS | ||
| PflFI | GACN[darr]NNGTC | N | ||
| (Tth111II) | CAARCA(11/9) | |||
| (UbaDI) | GAACNNNNNNTCC | |||
| (UbaEI) | CACCTGC |
Table 1. continued
| Prototypea | Isoschizomersa | Recognition sequenceb | Me sitec | Commercial sourced |
| VspI | AT[darr]TAAT | 5(6) | BDEFIR | |
| AseI | AT[darr]TAAT | AJNO | ||
| AsnI | AT[darr]TAAT | MS | ||
| PshBI | AT[darr]TAAT | K | ||
| XbaI | T[darr]CTAGA | 6(6) | ABCDEFGHIJKLMNOPQRST | |
| XcmI | CCANNNNN[darr]NNNNTGG | AN | ||
| XhoI | C[darr]TCGAG | ABCDEFGHJKLMNOPQRST | ||
| PaeR7I | C[darr]TCGAG | 5(6) | N | |
| (SciI) | CTC[darr]GAG | |||
| Sfr274I | C[darr]TCGAG | I | ||
| XhoII | R[darr]GATCY | EMRS | ||
| BstX2I | R[darr]GATCY | DI | ||
| BstYI | R[darr]GATCY | BN | ||
| MflI | R[darr]GATCY | AK | ||
| XmaIII | C[darr]GGCCG | 4(5) | BE | |
| BseX3I | C[darr]GGCCG | I | ||
| BstZI | C[darr]GGCCG | R | ||
| EagI | C[darr]GGCCG | ?(5) | NP | |
| EclXI | C[darr]GGCCG | MS | ||
| Eco52I | C[darr]GGCCG | ADFKOR | ||
| XmnI | GAANN[darr]NNTTC | DENR | ||
| Asp700I | GAANN[darr]NNTTC | M | ||
| MroXI | GAANN[darr]NNTTC | I |
Type I restriction enzymes
| Prototype enzyme | Recognition sequenceb | Me sitec |
| CfrAI | GCANNNNNNNNGTGG | |
| EcoAI | GAGNNNNNNNGTCA | 2(6),-3(6) |
| EcoBI | TGANNNNNNNNTGCT | 3(6),-4(6) |
| EcoDI | TTANNNNNNNGTCY | |
| EcoDR2 | TCANNNNNNGTCG | |
| EcoDR3 | TCANNNNNNNATCG | |
| EcoDXXI | TCANNNNNNNRTTC | |
| EcoEI | GAGNNNNNNNATGC | |
| EcoKI | AACNNNNNNGTGC | 2(6),-3(6) |
| EcoR124I | GAANNNNNNRTCG | 3(6),-3(6) |
| EcoR124II | GAANNNNNNNRTCG | 3(6),-3(6) |
| EcoRD2 | GAANNNNNNRTTC | |
| EcoRD3 | GAANNNNNNNRTTC | |
| EcoprrI | CCANNNNNNNRTGC | |
| StyLTIII | GAGNNNNNNRTAYG | 2(6),-4(6) |
| StySJ | GAGNNNNNNGTRC | |
| StySKI | CGATNNNNNNNGTTA | |
| StySPI | AACNNNNNNGTRC | 2(6),-3(6) |
| StySQ | AACNNNNNNRTAYG |
Type III restriction enzymes
| Prototype enzyme | Recognition sequenceb | Me sitec |
| EcoPI | AGACC | 3(6) |
| EcoP15I | CAGCAG(25/27) | 5(6) |
| HinfIII | CGAAT | |
| StyLTI | CAGAG | 4(6) |
bRecognition sequences use the standard abbreviations [Eur. J. Biochem. (
| R = A or G | B = not A (C or G or T) |
| Y = C or T | D = not C (A or G or T) |
| M = A or C | H = not G (A or C or T) |
| K = G or T | V = not T (A or C or G) |
| S = G or C | N = A or C or G or T |
| W = A or T |
Recognition sequences are written from 5[prime] to 3[prime], only one strand being given, and the point of cleavage is indicated by an arrow ([darr]). When no arrow appears, the precise cleavage site has not been determined. For enzymes such as BciVI, which cleaves away from its recognition sequence, the sites of cleavage are indicated in parentheses. Thus GTATCC (6/5) indicates cleavage as shown below:
| 5[prime]-GTATCCNNNNNN[darr]-3[prime] |
| 3[prime]-CATAGGNNNNN[darr]-5[prime] |
In all cases the recognition sequences are oriented so that the cleavage sites lie on their 3[prime]-side.
cThe site of methylation by the cognate methylase when known is indicated as follows. The first number shows the base within the recognition sequence that is modified. A negative number indicates the complementary strand, numbered from the 5[prime] base of that strand. The number in parentheses indicates the specific methylation involved. (6) = N6-methyladenosine; (5) = 5-methylcytosine; (4) = N4-methylcytosine. Thus for Alw26I the designation 3(5),-4(6) signifies the following pattern of methylation:
| 1 | 2 | 3 | 4 | 5 | |
| 5[prime]G | T | 5mC | T | C | 3' |
| 3[prime]C | 6mA | G | A | G | 5' |
| -5 | -4 | -3 | -2 | -1 |
dCommercial sources of restriction enzymes are abbreviated as follows: A, Amersham Life Sciences-USB (4/97); B, Life Technologies Inc, Gibco-BRL (1/97); C, Minotech Molecular Biology Products (10/97); D, Angewandte Gentechnologie Systeme (10/97); E, Stratagene (4/97); F, Fermentas MBI (9/97); G, Appligene Oncor (10/97); H, American Allied Biochemical, Inc. (10/97); I, SibEnzyme Ltd. (4/97); J, Nippon Gene Co., Ltd. (10/97); K, Takara Shuzo Co. Ltd. (4/97); L, NBL Gene Sciences Limited (5/97); M, Boehringer-Mannheim (10/97); N, New England BioLabs (10/97); O, Toyobo Biochemicals (7/97); P, Pharmacia Biotech Inc. (8/97); Q, CHIMERx (10/97); R, Promega Corporation (7/97); S, Sigma (10/97); T, Advanced Biotechnologies Ltd. (1/97). The date in parentheses indicates the most recent update.
eEnzymes that cut on both sides of their recognition sequence, such as BaeI, BcgI, Bsp24I, CjeI and CjePI, have four cleavage sites each instead of two. For example, Bsp24I cleaves as indicated:
| 5[prime] | [darr]NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN[darr] | 3[prime] |
| 3[prime] | [darr]NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN[darr] | 5[prime] |
This is described in Table 1 and some REBASE reports as Bsp24I (8/13)GACNNNNNNTGG(12/7). Thus the recognition site is excised in a fragment, 32 bp long, with 5-base 3[prime]-extensions at each end.
fEcoRII isoschizomers fall into two classes based upon their sensitivity to methylation. EcoRII will not cleave when the second cytosine in the recognition sequence is methylated to 5-methylcytosine whereas MvaI will cleave such a sequence. Isoschizomers of EcoRII that are like MvaI are indicated by +.
gMboI isoschizomers fall into two classes based upon their sensitivity to methylation. MboI will not cleave when the recognition sequence contains 6-methyladenosine whereas Sau3AI will not cleave when its recognition sequence contains 5-methylcytosine. Isoschizomers of MboI that are like Sau3AI are indicated by +.
hTaqII differs from other restriction enzymes in recognizing two distinct sequences: GACCG and CACCCA.
Table REBASE is updated daily. Each month, a set of REBASE data files are released publically and distributed to the scientific community, at no charge, via e-mail. They can also be retrieved by anonymous ftp (www.neb.com, in pub/rebase), WAIS (www.neb.com, port 210) or through the World Wide Web (http://www.neb.com/rebase ). These data files are ASCII text files, many of which are designed specifically for use with a variety of software packages such as GCG, IGSuite, GENEPRO, Staden, DNA Strider, Pro-Cite, PC/Gene, SEQAIDII, GENETYX, DNASIS, CAD Gene and Reference Manager. Other data files include a complete set of references, including abstracts, to papers on restriction enzymes and methylases; a list of all commercial suppliers of restriction enzymes and methylases, complete with contact information and a listing of enzymes they currently sell. New data files are constantly being added and each release of REBASE includes a monthly newsletter indicating that the files at the www and ftp sites have been updated, and listing new enzymes, newly available formats, enzyme name changes, etc. To join the mailing list or for more information, contact either author (e-mail: macelis@neb.com or A HREF=MAILTO:s>roberts@neb.com>roberts@neb.com
aThe recognition sequence is loosely defined as the sequence that normally flanks the intron or intein encoding the endonuclease. [darr] indicates cleavage on the strand shown; _ indicates cleavage on the complementary strand.bFor commercial sources see the legend to Table 1.
Enzyme
Sequence around one cleavage sitea
Commercial sourceb
I-CeuI
CGTAACTATAACGGTC_CTAA[darr]GGTAGCGAA
N
I-DmoI
ATGCCTTGCCGG_GTAA[darr]GTTCCGGCGCGCAT
L
I-PpoI
TAACTATGACTCTC_TTAA[darr]GGTAGCCAAAT
NR
I-SceI
AGTTACGCTAGGG_ATAA[darr]CAGGGTAATATAG
M
PI-PspI
AAAATCCTGGCAAACAGCTA_TTAT[darr]GGGTAT
N
PI-SceI
ATCTATGTCGG_GTGC[darr]GGAGAAAGAGGTAAT
N
PI-TliI
GTTCTTTATGCGG_ACAC[darr]TGACGGCTTTTA
N
Because of the new naming conventions for homing endonucleases (4) several enzyme names have been changed. Those affected are the homing endonucleases NOT encoded in introns. These now carry the prefix F- and are called `free-standing endonucleases'.
| Old name | New name |
| Endo.SceI | F-SceI |
| HO-endo | F-SceII |
| I-SuvI | F-SuvI |
| N-TevI | F-TevI |
| N-TevII | F-TevII |
In forming Table 1, all endonucleases cleaving DNA at a specific sequence have been considered to be restriction enzymes, although in most cases there is no direct genetic evidence for the presence of a restriction-modification system. The endonucleases are named in accordance with the proposal of Smith and Nathans (5).
We request that authors wishing to cite REBASE use this article as a general reference for the complete listing that is available electronically.
Special thanks are due to the many individuals who have so kindly communicated their unpublished results for inclusion in this compilation. This database is supported by the National Library of Medicine (LM04971).
This article has been cited by other articles:
ACKNOWLEDGEMENTS
REFERENCES
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Comments and feedback: www-admin{at}oup.co.uk
Last modification: 17 Dec 1997
Copyright© Oxford University Press, 1998.
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