XmaI Recognition Site
XmaI at a glance
5' C|CCGGG 3' 3' GGGCC|C 5'
| Recognition site | 5'-CCCGGG-3' |
| Cut | C^CCGGG |
| Ends | a 4-base 5' overhang (CCGG) |
| Expected frequency | about once every 4,096 bp in random DNA |
| Compatible ends | AgeI |
| Same site | SmaI (CCC^GGG) |
How to find XmaI sites in a sequence
- Paste a DNA sequence or FASTA record into the box above. XmaI is already entered under Only these enzymes.
- Tick Circular DNA for a plasmid, so a site that spans the end and the start is found.
- The map marks each XmaI cut with its position. Copy or download the output below it.
Frequently asked questions
What sequence does XmaI cut?
XmaI recognizes CCCGGG (written 5' to 3') and cuts the top strand at C^CCGGG.
Does XmaI leave sticky or blunt ends?
Sticky ends: a 4-base 5' overhang (CCGG).
Which enzymes leave ends compatible with XmaI?
AgeI. Their overhangs are the same, so the ends can be ligated to each other.
How often does XmaI cut?
A site like CCCGGG turns up about once every 4,096 bp in random DNA. Real sequences vary, so check yours above.
Restriction enzymes
Restriction MapAatII Recognition SiteAccI Recognition SiteAflII Recognition SiteAgeI Recognition SiteAluI Recognition SiteApaI Recognition SiteApaLI Recognition SiteAscI Recognition SiteAvaI Recognition SiteAvrII Recognition SiteBamHI Recognition SiteBclI Recognition SiteBglII Recognition SiteBsiWI Recognition SiteBspHI Recognition SiteBsrGI Recognition SiteBssHII Recognition SiteBstBI Recognition SiteClaI Recognition SiteDraI Recognition SiteEagI Recognition SiteEcoRI Recognition SiteEcoRV Recognition SiteFseI Recognition SiteHaeIII Recognition SiteHhaI Recognition SiteHincII Recognition SiteHindIII Recognition SiteHinfI Recognition SiteHpaI Recognition SiteKpnI Recognition SiteMfeI Recognition SiteMluI Recognition SiteMseI Recognition SiteMspI Recognition SiteNaeI Recognition SiteNcoI Recognition SiteNdeI Recognition SiteNheI Recognition SiteNotI Recognition SiteNruI Recognition SiteNsiI Recognition SitePacI Recognition SitePmeI Recognition SitePstI Recognition SitePvuI Recognition SitePvuII Recognition SiteRsaI Recognition SiteSacI Recognition SiteSacII Recognition SiteSalI Recognition SiteSau3AI Recognition SiteScaI Recognition SiteSfiI Recognition SiteSmaI Recognition SiteSnaBI Recognition SiteSpeI Recognition SiteSphI Recognition SiteSspI Recognition SiteStuI Recognition SiteSwaI Recognition SiteTaqI Recognition SiteXbaI Recognition SiteXhoI Recognition Site
More DNA and protein sequence tools
Reverse ComplementDNA to RNACombine FASTA SequencesSplit FASTA SequenceGenBank to FASTAEMBL to FASTAGenBank Feature ExtractorEMBL Feature ExtractorGenBank Translation ExtractorEMBL Translation ExtractorSplit CodonsRange Extractor DNARange Extractor ProteinWindow Extractor DNAWindow Extractor ProteinFilter DNAFilter ProteinGroup DNAGroup ProteinOne-Letter to Three-Letter Amino AcidsThree-Letter to One-Letter Amino AcidsDNA StatisticsProtein StatisticsCodon UsageCpG Island FinderDNA Molecular WeightProtein Molecular WeightProtein Isoelectric PointProtein GRAVYDNA Pattern FindProtein Pattern FindFuzzy Search DNAFuzzy Search ProteinIdentity and SimilarityORF FinderTranslate DNA to ProteinReverse TranslateReverse Translate a Protein AlignmentPCR Primer StatsPCR ProductsRestriction SummaryMutate for DigestPairwise Align DNAPairwise Align ProteinPairwise Align CodonsCodon OptimizationCRISPR Guide FinderTranslation MapPrimer MapColor Alignment by ConservationColor Alignment by PropertiesCodon PlotPlasmid Map ViewerRandom DNA SequenceRandom Protein SequenceRandom Coding DNARandom DNA RegionsRandom Protein RegionsSample DNASample ProteinShuffle DNAShuffle ProteinMutate DNAMutate ProteinGenetic CodesIUPAC Codes