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.
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][1])

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).

 [1]: 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