Frequently Asked Questions

This tool supports GFF3 (Generic Feature Format version 3) files.

Sample format:

##gff-version 3
Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Name=AT1G01010
Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010
Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1
Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1
Chr1 TAIR10 CDS 3760 3913 . + 0 Parent=AT1G01010.1

Supported feature types include gene, mRNA, exon, CDS, and UTR (five_prime_UTR, three_prime_UTR).

After uploading a file, you can search for the following in the search box:

• Gene ID (e.g., AT1G01010)
• Transcript ID (e.g., AT1G01010.1)

As you type, suggestions will appear automatically. Fuzzy search is supported, so you can search even if you don't know the exact ID.

Yes, you can customize the colors of the following elements in the preview screen:

• UTRs:

  Color of 5' and 3' untranslated regions

• Exons:

  Color of coding regions

• Introns:

  Color of intron lines

After changing colors, click the "Regenerate" button to update the diagram.

You can export in the following two formats:

• SVG (Scalable Vector Graphics):

  • No quality loss when scaling
  • Editable in Adobe Illustrator or Inkscape
  • Perfect for scientific publications

• PNG (Portable Network Graphics):

  • Raster image format
  • Adjustable DPI (72, 150, 300, 600)
  • Transparent or white background options
  • Great for presentations and web use

When exporting as PNG, you can adjust the DPI settings:

• 72 DPI:

  For web display

• 150 DPI:

  Standard print quality

• 300 DPI:

  High-quality print (recommended for papers)

• 600 DPI:

  Highest quality (for publications)

For SVG format, resolution is not a concern as it's a vector image.

Please check the following:

• Verify the file is in GFF3 format
• Ensure the file extension is .gff or .gff3
• Confirm the file content is properly formatted (tab-delimited)
• Check that required fields (seqid, source, type, start, end, score, strand, phase, attributes) are present

If the problem persists, try testing with a sample file.

Possible causes:

• GFF3 file does not contain mRNA features
• ID attributes are not properly set
• Parent attributes are not correctly linked

This tool builds gene structures based on mRNA features. Please ensure your GFF3 file has the proper hierarchy (gene → mRNA → exon/CDS/UTR).

This tool works on modern browsers:

• Google Chrome (recommended)
• Mozilla Firefox
• Microsoft Edge
• Safari

For the best experience, please keep your browser updated to the latest version.