Plasmid Map
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Plasmid map

A labeled pUC19 diagram. View it, download it, or map your own sequence.

pUC19 plasmid map

2,686 bp Circular DNA

Circular pUC19 map, 2,686 base pairs: the seven non-source annotations in NCBI record M77789.2, four features detected by exact sequence match and its unique cutters from 56 commercial enzymes
Solid: source annotations. Dashed: exact-match features. Brown ticks: unique cutters.View full-size map

Source: NCBI M77789.2. Coordinates are one-based and inclusive.

GenBank sequence
See the seven source annotations and exact coordinates
NCBI M77789.2 · one-based, inclusive coordinates
AnnotationPositionStrandLength
M13mp191–447Forward447 bp
Lac-operon1–230Forward230 bp
Polylinker233–289Forward57 bp
Lac-Operon290–447Forward158 bp
pBR322448–547Reverse100 bp
pBR322548–684Reverse137 bp
pBR322685–2686Reverse2002 bp
See the 4 detected features and 20 unique cutters
Detected by exact sequence match · one-based, inclusive coordinates
FeaturePositionStrandMatches NCBI annotation
CAP binding site94–131ForwardJ01636.1 · regulatory note "cap protein binding site" · 1162..1199
lac operator178–198ForwardJ01636.1 · regulatory note "lac repressor protein binding site" · 1246..1266
AmpR (bla)885–1745ForwardY14837.1 · CDS gene bla · complement(1650..2510)
pMB1 replicon (ori)1905–2519ReverseY14837.1 · misc_feature note "replicon of pMB1" · 876..1490

Unique cutters, top-strand cut after base: HindIII 233 SphI 243 PstI 249 SbfI 249 SalI 251 XbaI 257 BamHI 263 XmaI 268 SmaI 270 KpnI 276 SacI 282 EcoRI 284 KasI 445 NdeI 498 AatII 753 SspI 867 ScaI 1191 BsaI 1606 PciI 2560 SapI 2677

How to read this plasmid map

A plasmid map places named regions and restriction sites along a DNA sequence. The circular line represents this molecule’s 2,686 base pairs. Positions count from the record’s first base; an arrow shows the direction of an annotation on its strand. The drawing is a sequence reference, not the physical shape or scale of a DNA molecule.

This example uses pUC19, NCBI record M77789.2. Its polylinker runs from bases 233 to 289, a 57-base interval including both endpoints. The pBR322-derived annotations run on the reverse strand. Overlapping annotations describe some of the same bases in different ways. Expand the coordinate tables above to read the exact intervals.

Solid shapes are annotations deposited in that record. Dashed shapes are features found by exact sequence matching: AmpR, the pMB1 replicon, the lac operator and the CAP binding site. These are labeled separately because a sequence match does not verify a construct or its function. The sources and methods explain the annotation and matching rules.

Brown ticks mark enzymes that cut once in this sequence among the 56 enzymes checked. Each number names the base after which the top strand is cut. Use the restriction digest calculator to inspect cut positions and fragment lengths for your own sequence.

Make a map of your own plasmid

Open the plasmid map editor to import GenBank, FASTA or SnapGene .dna files, inspect circular and linear maps, and download a map as SVG or PNG. Choose Try example there to explore this same pUC19 record. Your files and projects stay in your browser; the editor does not upload your sequences.

For a sequence you are working with, the ligation calculator calculates insert mass from an insert-to-vector ratio, and the oligo calculator provides sequence mass and DNA copy-number calculations. Each tool states its assumptions beside the result.