Video

https://youtu.be/f5s0IP7FZKc

The lab reports are a training to write scientific texts and an important part of the course. To pass you need to provide a final version of the lab report within 7 days after the lab. You have one chance to submit a preliminary version and receive feedback on it (not mandatory). The preliminary version needs to be submitted within 72 hours of the lab and feedback will be provided at the latest 24 hours before the deadline of the assignment. If the final report it not submitted in time or it contains an error you will get an Fx on the lab course.  This means that you have to submit an updated lab report within 7 days after the exam and that the highest grade you can get is an E on the entire course. If this does not occur you will have to re-register for the course next time it is given (normally next year) and complete the missing parts that year and you can still not receive a grade higher than E.  So in short this is the rules for the lab reports.

Instructions

Answer all questions and send it to Marco by email.

***Please send a pdf file (not .docx, .odt etc) with “name_lab_your_name.pdf”

General instructions:

* You should do this assignment on your own. Only ask the assistants if something is really unclear.
* The assistants will pass bye the lab twice during the day.
* Any other internet resource is allowed.
* You are allowed to copy the results but not the description of methods.

You have obtained a domain of a protein sequence, this should be used as a start for all assignments. Your task is to identify the protein and find out more about it. For all questions it is important that you provide not only the answer to the question but also the data supporting your claim (i.e. copies of results) and a description on how you obtained the answers. Further, a description on how reliable you think the answers are important for full credits.

Note: The sequence you have got might not be the “full length” protein but just one domain. Some questions are related to exact the sequence you got and some to the full lenght sequence

Questions about your sequence:

1. What Pfam domain does this sequence you got match?

2. What is the secondary structure of your sequence ?

3. Identify possible interaction partners of your protein domain. What is  the evidence for that ?

4. Identify the full length protein.  What is the name and UniProt ID of the protein ? Which organism does it belong to?

5. What PDB files are homologous to your protein. Make a model of as long part as possible of your protein. Upload a picture of the model as a part your answer.

6. Find the closest protein in mouse. What is the sequence identity ?

7. What is the annotation score and evidence for the full length protein ?

8. What is the sub-cellular location of your full length protein?

9. What is the molecular function of your full length protein ? Please provide the relevant GO-terms.

10. Use Ensembl to find possible splice forms of your protein. How many splice forms exist ?