Protocol Online logo
Top : New Forum Archives (2009-): : Bioinformatics and Biostatistics

Exons and introns NCBI-HOW?? - (Mar/16/2011 )

I am a molecular bio student and we have to come up with the structure of 3 genes (we are working on physical mapping). We are working with the dog genome project (13179) and I have to pick 3 genes off of chromosome 2. SO...I am looking at GAD2 (Gene ID: 487107) in do I find the introns and exons?

I went to ensembl and there are 3 transcripts for this gene, and they don't match up base pair wise (close but not exact), nor do I know which transcript is the right one. So I don't think I have the right information that my professor wants. I have clicked on just about everything there is to click on, but I can't come up with the introns and exons in NCBI. I read somewhere that when you click on the mRNA, there should be a gene table link...I don't see this. Can someone please explain where/how I do this.



If you got to the gene page for Gene ID 487107, and click on where is says "Go to nucleotide" selecting the GenBank option, it'll take you to here, the GenBank page for the reverse complement of basepairs 10,256,107 through 10,341,918 of chromosome 2 from Canis familiaris (accession NC_006584).

This GenBank entry has the information you need -- to go from the 85,812 bp gene shown to the 1,758 bp mRNA sequence, follow the directions listed in the GenBank file under "mRNA", e.g. join 1..123, 832..891, 1086..1235, etc.

These are the coordinates of the exons; anything between them (e.g. 124..831, 892..1085, etc.) are introns...


I see. I guess i was expecting something graphical and I wasn't sure about those. Thank you so very much fot taking the time to answer a basic question :-)