What does it mean when a published paper expresses a SNP by (for example) +45T>G, +276G>T, -420C>G in a specific gene? How can I find the rs # for these SNPs to be able to analyse them?
These indicate the position of the SNP relative to the TSS (transcription start site), upstream is denoted by (-) and after the TSS it is (+). Finding the rsID for these previously reported SNPs is a challenge.
You can try a google, pubmed search and sometimes hopefully you get a rsID.
Otherwise, may be you can get the gene sequence from Genbank and the TSS from Ensembl or Genbank. Copy the sequence region where your desired SNP lies and then go to dbSNP and search if there is any SNP in that region. You can get a FASTA file showing all possible rsIDs. Then you can do a BLAST to see which sequence match your sequence and get the rsID. A long procedure but will give you an answer.
Normally, the SNPs are also annotated in Ensembl. You can go to Ensembl, search for your gene of interest, choose the transcript of interest and then click in the left menu bar on "sequence" (probably cDNA sequence). The sequence will be displayed, you have to search for the positions you are interested in. Variations are indicated by different colours and the ambiguity code, if you mouse over the position in question, the rsID pops up, if there is one annotated.
I tend to Google the name of the gene followed by the position of the variant. Usually, you would get the rs#. I also tend to be paranoid and always verify it with dbSNP after obtaining the rs#. That would also be part of your analysis, to find predictions for what are the possible biological implications from the change in nucleotide.
The + and - sign denote how far away by nucleotide position is your variant relative to the start site. The > sign denotes wildtype nucleotide > variant nucleotide e.g. if G>T, it would be G as the wildtype and T as the variant.
Dear Manar, I recommend to try the SNPedia http://www.snpedia.com
For example, you search for +45T>G in the search box
Result: you will see a number of links. Check one of them i.e. "Association of the +45T>G and +276G>T polymorphisms in the adiponectin gene with insulin resistance in nondiabetic Greek women"
Then you check this link: http://www.ncbi.nlm.nih.gov/pubmed/19755407?dopt=Abstract
Result in PubMed abstract: ADIPOQ; +45T>G, rs2241766 and +276G>T, rs1501299
I hope this search algorithm will be helpful! I do so!
- Badges
- Science topic
- Similar topics
- Correction