Exon-Intron Graphic Maker
 by nikhil bhatla, nikhil@superfacts.orgnikhil.superfacts.org
 more web apps at WormWeb.org
 updated Apr 10, 2012 (version 4)


(If you don't know what this is all about, but you're curious, read my blog post for an introduction.)

This is a tool for quickly making proportional, publication-quality graphics that display your gene's important parts: 5' UTR, coding sequence, 3' UTR, mutations, deletions and domains.

In the 5' UTR, coding, and 3' UTR text boxes, copy and paste the exons and introns from your DNA sequence. The exons and introns can be distinguished in 2 ways:

  1. Enter exons as UPPERCASE and introns as lowercase, or
  2. Enter exons and introns separated by commas
As you add sequence data, the image below will update in real-time.

Space characters are ignored. All other characters are counted to make the proportional gene model.

In the marker locations section, you can specify sites of mutation and regions of deletion. To specify sites of mutation, just enter a location as the number of bases from the beginning of the gene (the first base in the 5' UTR is base 1). The marker will appear as a downward arrow. To specify deletions, just enter two locations separated by a dash. The deletion will appear as a horizontal line below the graphic. You can also provide a label for each annotation.

In the domain locations section, you can specify the sites of protein domains. Just enter two locations separated by a dash. The locations should be in amino acids, not bases (the start codon ATG methionine is amino acid 1).

For both the marker and domain locations, the available colors are black, red, green, blue, orange, purple, and gray.

In the scale length text box, you can specify the size of the scale bar. The default size is 100 bases. The thin line shown above the graphic is a scale bar. If you enter fewer bases than the length of the scale bar, the scale bar extends beyond the displayed area.

When you are finished, just right-click on the image to save a PNG, or click the button to download a publication-quality PDF. This PDF can be edited in a program like Adobe Illustrator or Inkscape (which is free).

If you want to leave a comment or ask a question, check out the blog post.

Note: If you're using Internet Explorer, the latest version of this web-app won't work, so please use the old version.

Tip: To convert selected text to all caps or all lowercase, use Shift+F3 in Microsoft Word (thanks Niels)

Gene name:
5' UTR sequence:
Coding sequence:
exons UPPERCASE and introns lowercase, or
separate with commas
3' UTR sequence:
Marker locations:
in bases; start counting from the 5' UTR
Label: Location: Color:
Add another marker
Domain locations:
in amino acids; start counting from start ATG
Label: Location: Color:
Add another domain
Scale length: