Enhance transgenes

Transgenes typically have all, or all but the first, intron removed. Still, splicing at cryptic splice sites occurs. This is linked to remnant exonic splice enhancer motifs. Removing these motifs alongside with other unwanted functionality will thus improve transgene efficiency.

Enter your sequence

Enter CDS

Enter Genbank or FASTA sequence
Complete Genbank or FASTA entries. FASTA entries must specify exons in upper case and introns in lower case.
Or, upload file
Plain text file in Genbank or FASTA format.
Or, load sample data

Use Homo sapiens hemoglobin subunit beta (HBB) CDS as sample gene.

Enter 5'UTR

Enter Genbank or FASTA sequence
Complete Genbank or FASTA entries. FASTA entries must specify exons in upper case and introns in lower case.
Or, upload file
Plain text file in Genbank or FASTA format.
Or, load sample data

Use Homo sapiens hemoglobin subunit beta (HBB) 5'UTR as sample gene.

Enter 3'UTR

Enter Genbank or FASTA sequence
Complete Genbank or FASTA entries. FASTA entries must specify exons in upper case and introns in lower case.
Or, upload file
Plain text file in Genbank or FASTA format.
Or, load sample data

Use Homo sapiens hemoglobin subunit beta (HBB) 3'UTR as sample gene.

Enter ESE motifs Optional

Enter motifs
DNA sequence motifs of 5-10 bases, one motif per line.
Or, upload file
Plain text file containing one motif per line.
Or, select dataset

Enter restriction sites Optional

Enter sites that should be kept intact

Enter motifs
DNA sequence motifs, one motif per line.
Or, upload file
Plain text file containing one motif per line.
Or, load sample data

Use BamHI and EcoRI restriction sites as sample.

Enter sites that should be avoided

Enter motifs
DNA sequence motifs, one motif per line.
Or, upload file
Plain text file containing one motif per line.
Or, load sample data

Use BamHI and EcoRI restriction sites as sample.

Select parameters Please provide a valid CDS sequence first

Select a strategy
Select a strategy to select the best generated variant by its GC3 content
Select how to adjust ESE resemblance near introns to be removed
Select which sites should be adjusted for ESE resemblance
Select if first intron should be kept or removed
Select how 6-fold degenerate sites should be treated

Submit your job Please provide a valid CDS sequence first

Your input data is not yet saved. Please click the "Save" button of each form you have put data into.

How to cite this web service

Stefanie Mühlhausen, Laurence D Hurst. Transgene-design: a web application for the design of mammalian transgenes, btac139, Bioinformatics (2022).