Hi all, I want to make the truncation of my gene, I divided the full length gene sequence into 7 parts (truncations), which is shown in the picture below. Is there any way or website to determine that which sequence of the gene should I choose for truncation or just I randomly cut it into different parts? I searched my gene on Uniprot website for Mesocricetus auratus but the sequence there is incomplete compared to NCBI and no domains or motifs sequence are given there. my question is can I just randomly cut it into different parts and see its effects as given in the picture?
Depends on the purpose of your experiment. If you intend to express and study the protein encoded by this gene, I would run some domain prediction software over the translated sequence and aim the cut points at domain boundaries. Also, you would have to be careful that all fragments remain in the correct reading frame.
Annemarie Honegger thank you for the answer, could you please recommend me some domain prediction software?
You might try:
InterPro
https://www.ebi.ac.uk/interpro/
DomFold/Intfold
https://www.reading.ac.uk/bioinf/DomFOLD/ https://www.reading.ac.uk/bioinf/IntFOLD/
SMART
http://smart.embl-heidelberg.de
PROSITE
https://prosite.expasy.org
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