Question about how fetch intron location

Question

[jesselee516]

Merry Christmas and Happy New Year,

Hi,I am new to this research.I am trying to understand how to fetch intron location.I have get gene location and exon location from NCBI, but I am still confused about exon location. My question could be shown as follows:

Structure1: 5'UTR -> exon -> intron ->exon->intron->exon-> 3'UTR

Structure2: 5'UTR-> intron->exon->intron->exon->intron->3'UTR

Q1: when I only consider intron location, whether I do not consider 5' or 3' UTR as intron? What I mean is 5'UTR or 3'UTR is not the same as intron.

Q2:As we learned, Structure1 is usually structure for gene.However, is that possible in Structure2? 5'UTR is adjacent with intron, but not exon.From NCBI .gff download file, I only could get gene location and exon location. If Structure2 is possible, how do I define intron location without 5'UTR location?

Thanks for your help.

[Pierre Lindenbaum]

An Intron is always localized between two Exons. "Structure2" is a nonsense.

[Ram]

Why is Str2 nonsense again? I'm either horribly disoriented or horribly mistaken.

[Pierre Lindenbaum]

an UTR followed with an INTRON?

[Ram]

Yes, why not? I'm talking about genomic sequence. Perfectly possible for an entire exon to be a UTR, in which case an intron follows it.

[Pierre Lindenbaum]

oh yes sorry. I'm stupid :-P

[Ram]

Not at all. You just made me question my meager knowledge for a minute, that's all :)

Answer 1

[Ram]

Here we go, this is the way I see the definition a few of the terms used in your questions:

Exon: genomic sequence that is transcribed to pre-mRNA mature mRNA

Intron: genomic sequence that is not transcribed to pre-mRNA mature mRNA

UTR: mRNA sequence that is not translated to protein (hence, the name - un-translated region)

UTRs can be as short as a few bases to as long as multiple exons. (IIRC A4GALT1 has ~3 exons worth of 5' UTR - see here)

So, we can conclude that a UTR can span an exon and hence can be followed by an intron. Both Structure 1 and Structure 2 are valid. Let's now tackle the problem once you're clear with this understanding. Exon co-ordinates should now give you UTR co-ordinates as well, but the challenge is to find out which part of the exons are UTR (AKA the translation start site position).

[Siva]

Intron: genomic sequence that is not transcribed to pre-mRNA

Did you mean to say genomic sequence that is not present in the mature mRNA? Because pre-mRNA refers to the transcript before splicing and it does contain transcribed introns.

[Ram]

Yes, that's what I meant. I apologize. Thank you for the correction!

[jesselee516]

Thanks for your detailed answer. It did help me a lot. Happy new year.

[Ram]

You're most welcome. As someone who went through the learning process recently, I understand how these terms can get a little confusing at times. Oh, and a happy new year to you too!

[jesselee516]

By the way, from my download .gff file, I only could get the exon location.As you describe, could I just consider intron location as a location between two exon location.No matter how many exon UTR could span or UTR does not span exon, location between two exon could be considered as an intron location, is that right?

[Ram]

Exons and introns are differentiated at a different level than coding and UTR regions. The former differentiate regions that do and do not get transcribed, while the latter differentiate the regions that do and do not get translated.

So, operating on a genomic sequence level, all we need be concerned with are exons and introns, and they always alternate. Once the exons are spliced together, we can think about UTRs and CD exons.

So yes, introns are bounded by exons. On a forward strand gene, intron1 starts from end_position(exon1)+1 and ends at start_position(exon2)-1

[jesselee516]

Thank you very much for your answer. I understand it very clearly.

[Ram]

You're welcome :)