Exon intron boundaries - where to check those (Jan/30/2006 )
I want to design primers to amplify the exons of a gene.
How can I find information about the exon /intronic boundaries of the gene?
I know for instance I can dowload vector sequences with the information available like promoter region, antibiotic resistance gene, etc.
Can I download the gene sequence with the defined exonic boundaries ?
yes ucsc genome browser-- click on your gene in the map and then there should be a link for the complete genomic sequence---look around if you don't find I'll look one up and give more specific directions for the link... usually they will show exons in like blue or red and introns in black sequence...
Meanwhile I found in this website and it worked!
Typing the gene name I could get the Ensembl gene number,
clicking on that I could see a link " Exon information"
and indeed get all exon (in black) and intron (i blue) sequences.
Finally I could get it and design the primers!
Both NCBI and Embel have display the gene and ORF information for nucleotide sequence. For designing primers on the exon-intron or exon-exon boundaries, try having a look at this software