How to find an EXON - (May/01/2006 )
Hello every one,
I would be thankful if any one can help me in this.
In my project I have to find a mutations in a gene so I have to extract DNA and then go through PCR ..etc.
My problem now is that after I found the primer from the NCBI and from several papers , my supervisor refused to consider it because it was mRNA sequence and she wants the DNA sequence!!!.
Frankly I am not sure if this is correct or now, because I am still learning 
, but my first problem that I can not find such sequence from the DNA. Of course I can write the cDNA, but I am wondering if there is another way to get the DNA sequence for the primer.
My second problem , which is more difficult for me, that she wants to know that this sequence referring to which exons in the gene. Here I totally get lost because I do not know how to search for the exons.What I know is that the gene I am working about is contains 20 exons.
So pleaseeeeeeee can any one of you have any idea how he can help me.
Thanking you all, 
I think maybe I can help you for the first part of your question for sure...
you can blast with your cDNA sequence to obtain the genomic sequence. right by the accession number, the next line is a description of the sequence source...you just find a sequence which contains the complete gene with the source being chromosomal DNA clones, not cDNA, and there you are. this only doesn't work if the area of the genome for which you search has not been sequenced yet...does this make sense? I'm not sure if I have explained it properly.
for the second part, I am not sure of the best way to help you? you can compare the cDNA with the gDNA and look for differences, but that will not necessarily take all factors into account and will only give you a rough idea
you can blast with your cDNA sequence to obtain the genomic sequence. right by the accession number, the next line is a description of the sequence source...you just find a sequence which contains the complete gene with the source being chromosomal DNA clones, not cDNA, and there you are. this only doesn't work if the area of the genome for which you search has not been sequenced yet...does this make sense? I'm not sure if I have explained it properly.
for the second part, I am not sure of the best way to help you? you can compare the cDNA with the gDNA and look for differences, but that will not necessarily take all factors into account and will only give you a rough idea
Dear Aimikins,
Thank you for your interesting.
Actually , I could not under stand you 100%. Do you suggest to take this sequence and search for blast for it???
Otherwise, can you please put the link where I can start.
Thanking you in advance.
this is Blast for nucleotides (blastn)
plug your sequence into the box and wait for the matches to pop up...this is from NCBI's site; are you not familiar with Blast?
sorry for being late.
It is OK now.
I know this option already but I found that my supervisor was trying to examine me so she wanted a very complex way to get the same result.
Any way thank you for your help and sorry for being late