The answer should not be an extensive essay with excessive discussions. The facts should be put together in a logical context with (adequately sized) introduction and a
conclusive summary. 
Answers should cover the relevant aspects listed below. Not all aspects/questions are applicable in some cases. 
The text should define the major features of the mRNA, gene and protein.
Precision of descriptions is more important than lengthy discussions 

it should not be a pure listing of “bulletpoints” 

Finally, You may highlight the importance of the gene/mRNA (Summary) and the most
important findings of your analysis. 
The answer may contain figures or schematic drawings. Figures should be accompanied by adequate figure legends which describe briefly, but clearly the main content of the figure/scheme shown.The origin of data and references used should be listed (Reference list).
2015/16 BIO-M209

DATA HANDLING LINKED TO MOLECULAR MEDICINE

Coursework 2:

Genes and databases
(Retrieving informations on genes and DNA sequences)

Starting experiment:

During a project to identify regulated genes in cell lines derived from various human cell lines (Normal, diseases) and mouse disease models, cDNA libraries were established from isolated mRNAs. Multiple clones were isolated by various criteria like differential expression or similarity between species. Some selected “EST” fragments (01 to 17) were not identified and their identity remains therefore unclear. It should be mentioned that the mRNA preparation may also contain small amounts of genomic DNA.

Task in the coursework:

Every student receives a sequence without an explicit hint on the identity of the sequence provided, the corresponding gene or the function of the protein. The sequences will be found on Blackboard/BIO-M209/Coursework 2 and can be retrieved acc. to the number selected.

The DNA sequence should now be analysed in more detail. Informations from various databases should be used to identify the mRNA, its coding gene, define the genomic location of the sequence fragment and of the potentially encoded protein. This will help to further draw conclusions on any encoded protein, its structure, the physiological functions of the protein and correlations with (human) diseases. Any unusual sequence features or mutations should also be identified (if applicable).

The databases discussed in the lecture/seminar of BIO-M209 can be used. Informations can be found in the lecture/seminar material or in a compiled list of potentially useful databases (see Blackboard).

Format of the answer

 The answer should not be an extensive essay with excessive discussions. The facts should be put together in a logical context with (adequately sized) introduction and a

 conclusive summary. 

 Answers should cover the relevant aspects listed below. Not all aspects/questions are
 applicable in some cases. 

 The text should define the major features of the mRNA, gene and protein.
  Precision of descriptions is more important than lengthy discussions 

 It should not be a pure listing of “bulletpoints” 

 Finally, You may highlight the importance of the gene/mRNA (Summary) and the most
 important findings of your analysis. 

 The answer may contain figures or schematic drawings. Figures should be accompanied by adequate figure legends which describe briefly, but clearly the main content of the figure/scheme shown. 
  The origin of data and references used should be listed (Reference list) 

 Links to databases and other resources may be found in the lecture on “Databases” 

Questions to be asked

These are suggestions for questions to be asked (Feel free to find more) Not all questions may be applicable to some sequences

Part 1: Identification and characterization of the gene and protein Identification

Describe briefly your approach to identify the identity of the sequence Name the corresponding gene and the species where it is derived from Are there any indications of gene families or related genes/proteins?

Homologies with similar proteins in other species? Indications of evolutionary relationships (see also below)?

Genetic locus

Define the chromosomal location Genetic locus and its surrounding genes

Gene organization

Define the gene organization (Size, exons, intron etc). Indications for multiple transcripts? How are they generated? (- if applicable) Define the coding exons.

Is there alternative splicing? Define the specific differences

 Transcript(s) / mRNA 
 Transcribed mRNA(s) 

Relationship of multiple transcripts (if applicable) Descriptions of special features of the mRNA sequence
 Unusual sequences? Mutations? 

 Encoded protein(s) 
Define any protein(s) which may be encoded by the gene/mRNA

If there multiple proteins encoded (if applicable) define their relationship Name some characteristics of the protein (like Structure, Domains, Complexes) Unusual protein sequences included?
Protein structure

What is known on the general protein structure? Anything known on multimerisation (- if applicable) Special structures?

Interactions with other proteins (- if applicable)

Protein functions

Categorize the protein (Example: Transcription factor) Major functions of the protein(s)

Specific role in metabolism and cell function
Mutations / Diseases

Are sequence variations (Mutations, SNPs etc) included? Known mutations or polymorphism indicated in the data set? Relevance of some of these variants (if applicable)

Potential links with mutations and (human) diseases Any other medical or scientific relevance of the protein?

Other species

Is the gene/protein also found in other species? Evolutionary relationship

Are there mouse models available? (if applicable)

What are major phenotypes in mouse mutants? (select typical symptoms) (Database example: “jaxmice.jax.org”)