I need a little help in naming of SNP. What does "1123" indicates in SNP name, such as -1123C/T? Does this mean upstream of starting point (ATG) or from exon 1?
Dear Sailesh
that mean your single nucleotide change occur within the position of 1123 from the sequence of exon 1 of your gene which is C may change to T as a single necleotide polymorphism ,if you have the rs number of your SNPs may i can help you more
In attachment you can find an example for that
best regards
Hi Sailesh,
Generally, this way of mentioning SNP indicates that -1123C/T is change from C to T at -1123 bp of promoter region from the first bp of 5'-UTR.
This is not the case always. In few cases, it can indicated from the start codon ATG.
As per our experience, this way of representing SNP is little bit confusing. There is one of the best way that gives all information about SNP of your interest. For that you have to look for the permanent identification number of that SNP (it starts with rsXXXXXX) from the related literature. If you have rs number then you can get all information about its location, distance from the start codon etc... on the web-servers like dbSNPs (http://www.ncbi.nlm.nih.gov/SNP/) or ENSEMBL (http://www.ensembl.org/info/genome/variation/index.html). Find out the rs number for your SNP.
I hope this helps you
Thanks
Dear Tao,
Actually i don't know if there is a direct way to do that , i depended on ensembl database in my study and get the rs of the SNPs by below steps:
1- Find the website:http://www.ensembl.org/index.html .
2- choose the species type and the name of your gene
3- By the left of the page " Gene-based displays " go to sequence option then chose cDNA you will see page like the one in the attachment
4- finally you have to go to the the position of your SNP by looking for the codon in which your SNP within and you will see letter upon the base which have change according to the description, like "-1123C/T" when you stop the mouse on it the" rs" will appear.
please refer to the example in attachment picture.
i hope this useful...
Good Luck
Dear all,
I would be very grateful if someone could help me to figure out location of the upstream variant -1438G/A (rs6311). In particular, I am intetrested if -1438 relates to bp upstream from the start codon or from the core TSS. Many thanks in advance.
There are many ways to know the SNP location exactly, NCBI consider the best one due to its simplicity and furthermore there is ensembl website it also can predict the position of SNP, https://www.ncbi.nlm.nih.gov/snp/?term= and http://asia.ensembl.org/Homo_sapiens/Info/Index respectively
In (-1123C/T) SNP: 1123 is location of SNP in gene, (-) indicates upstream variant from transcription start site (+1) and C allele can be replaced by T allele. This can be searched in dbSNP from NCBI, that is available completely free of cost.
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