Exon + Intron Sequence - (Feb/06/2008 )
I am afraid my question is a bit stupid.
I want to get the sequence of my human gene containing exons + introns. I perfectly get the mRNA or coding sequence of my gene, also the complete chromosome its on - but what I need is something between- the sequence starting with exon 1 - containing all the exons & introns - ending with the last exon.
Can somebody recommend me a database please ?
you can use the Genome Browser at UCSC for this (http://genome.ucsc.edu/), just BLAT your cDNA sequence, the program will align this to the genome (click details for the complete sequence of the genomic sequence with the exons highlighted), for a graphical overview, click browser and subsequently click DNA (menu bar on top), then you get the DNA sequence currently displayed graphically in the browser
Best tool is AFAIK Ensembl, you search for your gene, choose a transcript and then it's Exon view, you will see all the exons and intron sequences between them (use a checkbox for a full intronic sequence).
Thank you dpo and Trof for your answers, that was the information I was looking for.
My new question: Trof, is it possible to export the intron sequences from Ensembl e.g. in FASTA format ? (I could not)
Not that I know of. I just copy them into the text file, it's very close to FASTA and can be used for most applications same way.
Yes you can. It is possible via the front end AND the backend SQL database.