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introns and exons

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introns and exons

Postby kai85 » Sun Mar 29, 2009 2:42 pm

Hello,
I am currently taking a biology module for my general education requirements. I have been trying to keep up with the text and lectures but am still stuck at my assignment. I hope this forum would be of some help to me. :D

1. In the context of a new mammalian model organism recently sequenced and annotated, gene YFG has 3 introns and 4 exons. Databases show that there are 3 different lengths of cDNA sequences associated with Gene YFG. One of these cDNA sequences has three out of four exons plus additional nucleotide sequence at the 3’ end of the cDNA. This part codes for an extra 123 amino acids. Annotated gene UB2, appears immediately downstream of YFG. UB2 has a single exon coding for 123 amino acids matching the cDNA. There is no cDNA in your database encoding for a UB2 gene with these 123 amino acids at the N-terminus.

A. Is UB2 justified as being a separate gene? Explain why or why not.
B. Draw a picture of YFG’s most likely intron/exon organization.

A.
I would think that UB2 is not a separate gene of YFG because it appeared 'immediately', hence suggesting that the coding of the 123 amino acids had something to do with the formation of gene UB2.

However, I am not too sure about my answer because I do not understand where 'downstream' is. Does this mean it's at the 3' or 5' end?
I have tried going through my textbook and lecture notes again but to no avail. And I have also tried asking on my module forum but with no replies. I am not asking for an answer to copy but maybe some questions and directions for me to think about and helps me in my formation of an answer.

I have also attached a picture of how I would draw YFG's intron/exon organization. I think it is correct, but the question's wording is a little confusing and I am quite doubtful. I am assuming that the question wants us to draw an organization that has not yet been spliced, so I included the introns and also the G-cap and poly A tail.

I hope this doesn't sound like I'm asking you guys to help me do my homework, but I am really confused and would appreciate any help given. :D Thanks!!
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Postby yrfaith » Tue Mar 31, 2009 11:13 am

Hi Kai85

It would appear that we are taking the same module. I came online to look for solutions and stumbled on your post.

How does appearing immediately downstream justify it not being a separate stream? in any case, downstream is 5' to 3' i'm quite sure.

may I add that this module has turned me off bio forever. I cannot imagine what possessed the professors to offer it as a General Elective even to people without a background in A levels biology. bloody stupid if you ask me or my 5 other friends struggling with the same module.
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Postby kai85 » Tue Mar 31, 2009 1:45 pm

Hello yrfaith,
I am still quite confused about the whole question. Do you think it is a separate gene? I've been trying to read my textbooks but am very frustrated because I really don't know how to answer the question.

It's lucky that you have friends taking the module with you! I am alone and have no friends with bio background :( I am trying very hard but it's not working....

Perhaps we can discuss the question here? The forum doesn't seem to be too helpful with the annoying troll around.
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Postby canalon » Tue Mar 31, 2009 4:48 pm

A- Downstrean means in the 3' direction of the gene (yrfaith is correct)
Read about alternative splicing of mRNA. In short in eukaryotic genes, during mRNA synthesis not all exons are going to the final mRNA, but a selection of them. This allow more than one product to be coded by a single gene. And this explain the different sizes of cDNA that are observed. And this should give you the answer to the question.

B- Your map should be of the DNA, no capping or tailing involved. Just introns and exons. You should also consider the answer to A, because it is important. Name your exons (YFG1 to YFG4) and locate UB2 on the map too.
Patrick

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Re: introns and exons

Postby kai85 » Tue Mar 31, 2009 4:59 pm

i re-read my post and realised that i seem to be referring to some troll in this forum! :oops: i was actually referring to the one in our module forum!

thank you for the hints canalon, i will definitely work on it tonight. i just hope i would be able to understand :x
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Postby canalon » Tue Mar 31, 2009 7:32 pm

If you have more questions, or you need clarifications, do not hesitate to ask.
Patrick

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Postby kai85 » Wed Apr 01, 2009 1:28 pm

hi canalon,
i do not understand why gene UB2 has to be included in my diagram because it appears only after alternative splicing of gene YFG. if i were to include it in the diagram, does it mean that the 1 exon that was not included in the splicing is gene UB2?

i also do not understand the last sentence of the question: "There is no cDNA in your database encoding for a UB2 gene with these 123 amino acids at the N-terminus." is this trying to say that UB2 gene actually does not exist? that it is just the 1 exon that was not included in alternative splicing process?

thank you in advance! :)
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Postby canalon » Wed Apr 01, 2009 4:07 pm

If I answer to the first question, I answer the whole exercise, which would be pointless.

But, alternative splicing in this case is the key. Read carefully:
Databases show that there are 3 different lengths of cDNA sequences associated with Gene YFG. One of these cDNA sequences has three out of four exons plus additional nucleotide sequence at the 3’ end of the cDNA. This part codes for an extra 123 amino acids. Annotated gene UB2, appears immediately downstream of YFG. UB2 has a single exon coding for 123 amino acids matching the cDNA. There is no cDNA in your database encoding for a UB2 gene with these 123 amino acids at the N-terminus.


What part of the protein is the N-terminus, beginning or end?
So what do you think is UB2. Remebre, annotation are just comments, they can be wrong.
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Re: introns and exons

Postby kai85 » Wed Apr 01, 2009 5:41 pm

hi canalon,
thanks for your hints. i think i know my answer now. ub2 is not a separate gene but the exon that wasn't included in the splicing process. it was annotated as a gene, but may not necessarily a gene. although there is no cDNA in the database encoding for the gene, the 123 amino acids are still coded from the exon. :D :D
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Postby canalon » Thu Apr 02, 2009 3:17 am

You got it. That is why it should be included in the map :)
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