Exon-Intron Graphic Maker
 by nikhil bhatla, nbhatla@mit.edunikhil.superfacts.org
 more web apps at WormWeb.org
 updated Nov 18, 2009 (version 3)

       

(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, and mutations and deletions.

In the 5' UTR, protein-coding, and 3' UTR text boxes, copy and paste the appropriate exons and introns from your DNA sequence. The exons and introns can be distinguished in either of 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 text box, you can specify sites of mutation and regions of deletion. To specify sites of mutation, just enter the locations as the number of bases from the beginning of the gene (the first base in the 5' UTR is base 1), separated by commas. The markers will appear as downward arrows. To specify deletions, just enter two locations separated by a dash (e.g. 145-678). The deletion will appear as a horizontal line below the graphic.

In the scale length text box, you can specify the size of the scale bar. By default, this is set to 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 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.

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

Gene name:
5' UTR:
Protein-coding:
exons UPPERCASE and introns lowercase, or
separate with commas
3' UTR:
Marker locations:
start counting from the beginning of the 5' UTR
Scale length:
bases