Question: Question about how fetch intron location
2
gravatar for jesselee516
4.8 years ago by
jesselee516100
United States
jesselee516100 wrote:

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.

gene genome • 2.0k views
ADD COMMENTlink modified 4.8 years ago by RamRS24k • written 4.8 years ago by jesselee516100

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

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Pierre Lindenbaum123k

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

ADD REPLYlink written 4.8 years ago by RamRS24k

an UTR followed with an INTRON ?

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Pierre Lindenbaum123k
1

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.

ADD REPLYlink written 4.8 years ago by RamRS24k

oh yes sorry. I'm stupid :-P

ADD REPLYlink written 4.8 years ago by Pierre Lindenbaum123k

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

ADD REPLYlink written 4.8 years ago by RamRS24k
3
gravatar for RamRS
4.8 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

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: http://genome.ucsc.edu/cgi-bin/hgc?hgsid=402070773_F2iljTeLeSAU16aiC1Xcp2NRZaug&g=htcCdnaAliInWindow&i=NM_017436&c=chr22&l=43088126&r=43116876&o=43088126&aliTable=refSeqAli&table=refGene)

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).

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by RamRS24k
1
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.

ADD REPLYlink written 4.8 years ago by Siva1.6k

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

ADD REPLYlink written 4.8 years ago by RamRS24k

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

ADD REPLYlink written 4.8 years ago by jesselee516100

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!

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by RamRS24k

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 matther 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?

ADD REPLYlink written 4.8 years ago by jesselee516100
1

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

 

ADD REPLYlink written 4.8 years ago by RamRS24k

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

ADD REPLYlink written 4.8 years ago by jesselee516100

You're welcome :)

ADD REPLYlink written 4.8 years ago by RamRS24k
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