Sequence for nucleotide 845 in HFE gene - (Mar/20/2015 )
I'm taking a class in which I bascially have to recreate a known molecular test. I've chosen to test the 845 G/A mutation in the HFE gene that is associated with hemochromatosis. The problem I'm having is finding the sequence used to determine the 845th nucleotide. I was able to find the sequence surrounding this mutation but cannot seem to find the starting point. I have a print out of the whole gene, and when I count 845 from the start this mutation is not present. Surely my inexperience is getting in the way, but I've been at this for many days and just am stuck. Please help!
Find the start codon. If you used the nucleotide site on NCBI, then look for CDS and the positions described.
Bob1 -
You are the best. You led me in the right direction and I found exactly what I need. Thanks for resolving this very frustrating situation for me. Hopefully it will be smooth sailing through the rest of my project! Thanks again!
Also, when working with sequences, it is very helpful to take advantage of the electronic text features.Printing and calculating nukleotides on paper is labourous and prone to mistakes.
Many text editors, even Word have option for character count. Also, electronic text is searchable.
Personally I use Notepad 2 for working with sequences, it has quick and easy option to join lines and replace spaces between sequences (often, when you copy a raw sequence it is in fixed-length rows with "end-line" spaces between them, Notepad 2 can make a continuous sequence out of that by two keyborad-shortcuts). I use Word for sequence anotations if necessary (you can use highlights and so), but Word itself has no good way to join all lines.
Other websites offer more comfortable coding sequence viewing. Try Ensembl, this can display cDNA with the respective codons below and it's very easy to find the righ sequence there. It also annotates existing SNPs into the sequence if you configure it so.