about size of genomic DNA - (Feb/27/2007 )
can any one know how to calculate size of genomic DNA of a particular protein
There are many ways to find out, but you can't just calculate the size of the region in genomic DNA from the size of the protein...
it depends for instance on how many introns there are, and how big these are.
Just as an example:
If you have no introns, and you know the amount of amino acids in the protein, then the genomic DNA region will have
three times that amount of bases, as three bases encode one amino acid.
(Say your protein has 180 amino acids and no introns; then the genomic DAN stretch encoding that protein has (180*3)= 560 bases )
Hope this helps, rather than cofuse you
after back translation of the protein, gel electrophoresis of the DNA against a standard..
maybe sequencing can help also
If you mean that you want to know how much of the genome is taken by your protein, you can access the Human Genome via PubMed Entrez (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) . There is a tab called "genome". Select it and you should be able to work your way through to find the size of the genomic DNA for your protein.
As an alternative, you could look at EXPASY (www.expasy.ch) and see what has been done on your protein.
thank you for your reply. i tried as you told but i didnt get result. for example if i want to know Homo sapiens NADPH oxidase 1 (NOX1) protein size of genomic DNA what to do. please tell me if you know. thanks in advance.
if you don't care about introns, then do as PFA-Goofy says and multiply amino acids by 3. if you want to know the size of the gene with introns and exons, swanny's suggestion should have worked. I can suggest another one though, if you go to UCSC genome browser, type in NOX1 it will show you position in genome then click on full name of gene (select the refseq or known gene). I selected known gene, the first on the list. now you see a picture of the intron exon boundries etc. click on the graphic at the top (the known gene again) this takes you to a summary page. in the first table select sequence. This will allow you to download the full genomic sequence (introns and exons) the exons only(exons only should equal the number of coding bases in the mRNA) or the mRNA with UTRs.
if you are doing this example and I have explained well you should find:
genomic size: 100,015,990 - 99,984,970=31,020
Protein 564aa (For x3 method =1,692)
genomic exons only (select CDs exons) =1,695 **cross verifies the X3 method (the extra 3 AA are the stop codon)
Hope this helps!! BTW-if this is the only one you have to do still verify make sure i selected the right gene etc, do not take my word for these numbers as i was rushing just quick example...