You will get a sequence, using your sequence you should answer the following questions:
1- Identify the name of the gene. Find out a complete cDNA.
2- Translate the coding sequence, find out if this translated protein belongs to any known protein family. See if you find out domain motifs or other features that gives you some information to reveal the function of this protein.
3- We want to make a vector construction, please make a nice restrictionmap with your cDNA first using all enzymes in Repbase and and secondly do 3 separate maps using only EcoR1, Hind III or Pst1.
4- We want also to isolate the 3´and 5´flanking regions of this gene, we do not have more sequence information, therefore it is of great help to search against the humandraft. Show 3 kb 5´and 3 kb ´3 of the start and stop codons.
5- A-Search the genomic location, find out other known genes in the near vicinity
B-Show GC-content, repeats, known ests, SNPs in the whole genomic sequence, add also 3kb from the ATG and 2kb from the TGA (or stop codon) (All in one figure).
6- Are they any other homologues in other species? Search with the DNA as well as the aminoacid you obtained in p.2. Any known functions in evolutionary distant species? (ex. fugu, zebra fish) How long in evolution can you go? Do a nice evolutionary tree. Finally make a nice picture of your protein sequences aligned to 3 other species homologues.
7- Try to find areas in the promoter that could be candidates to govern your genes expression pattern. (Align as many homologues as you can and use the adequate tools ex bl2seq, VISTA, RSA-tools to make your advanced analysis).
8- Find out if there is any information about the structure of this gene and despict on a 3D picture.
9- Is this gene involved in any disease? Make a resume of what is known about it.
10- Use the literature databases and give 10 key references.
11- Find out in which cell tissues your gene is expressed. Is the gene regulated in time? By hormones? etc.
12- Discuss how to proceed in the lab to corroborate the results you got with your computer analysis.
Hints: Use EnsEMBL, SRS, EMBOSS, Blast, InterPro, Genscan etc. Do not forget to do the same analysis using different services/program packages.
Presentation of projects:
1- The results must be presented orally and in a writen document. Prepare a nice document with your results, figures and conclusions (word and powerpoint).
2- Oral presentation: 10-15 minutes, present your conclusions with nice graphs and discuss how you got your results (tools, databases, parameters etc) and how you interpreted them. You must send your file latest one day before the presentation day.
Please fetch your sequence here:
