The gene that I work on has several large deletions in patients. I want to analyse the impact on the protein domains and also represent it in a figure.
If you know the protein sequence, you can use either PFAM or SMART. Else, if it is an unknow sequence, first translate your sequence using Expasy translate tool (http://web.expasy.org/translate/) and paste the protein ORF in the sequence window in the links given below. SMART not only gives protein domains, but also information on signal peptides, repeats etc.
http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1
OR
Sequence Search in http://pfam.xfam.org/
It seems you work on only 1 gene, then manually annotate it. You may first need figure out how many isoforms this gene has, then see if the truncations lead to frame shift, if so, you may have truncated protein, or early stop codon resulting NMD that leads the destruction of RNA. Then you better have western data as well. If it's still in-frame after truncation, you can calculate the location of truncation in amino-acid sequences, and as Savita suggested, see what domain you have in that region from START or ExPASy.
Dear Carina G Lechermeier
I have exactly the same question. Since I see there was no follow up, I created a new post asking this specifically: https://www.researchgate.net/post/What_are_the_best_available_tools_to_map_peptides_to_exons_automatically
I hope it gets more attention in this way :)
Hi, everybody!
1) browse your protein via Uniprot
2) take the information about the domains positions
2) found the external link via Uniprote site to NCBI Consensus CCDs database.
(https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi )
3) there will be a Nucleotide Sequence of mRNA of your protein with exon indication and a protein sequence with exon indication (in the same color)
5) make a superposition of domain and protein sequence with exon indication.
Hope that it will help you!
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