Protein Domains And Their Corespond Exons

Question

[Omid]

Hi all,

I have a human protein (NNT) which consist of three protein domains and also 22 exons.

I would like to know which exon/exons is translated to which protein domain. for example exon 2, 3 and 4 are translated to NADH binding domain.

I am not bioinformatisian and not familiar with programming so I am looking for a user friendly software to answer this question. Thanks

[Omid]

after searching I found Alamut software the best answer but it is not free available.

[Lalla]

Hi!

I have the same problem. In my case I have exons or part of exons diferentially expressed and their choordinates in the chromosome. I can find the sequence with Ensamble and translate them into aa sequneces but when I put them in Pfam or Interproscan5 I don't find any match. How can I know what is the specific information/function encoded by my exons? I am also new in bioinformatics, a user frindly tool would be highly appreciated! :)

Thanks

[Lalla]

another question: how do I interpret the information about the strand? For example I know that some of the transcripts studied are from the sense strand while other from the antisense one. When I am looking at the protein domains encoded by my exons I don't have to reverse in any case, because the coordinates are relative to the sense DNA, right?

Answer 1

[arnstrm]

If you know the sequence for your gene (whole genome), paste it on GeneMark to predict all exons (if you already have the exon information then skip this step). Paste each exon sequence separately on Pfam to detect the protein domain. If there is a domain in a particular exon, then you will get the information as well as beautiful graphics! I hope this helps.

Answer 2

[Khader Shameer]

I would recommend Ensembl annotations for these type of task.

Here you go:

[PoGibas]

Does UCSC has protein domain track?