SNP locus - SNP distance (bp) to major transcription initiatio (Dec/30/2004 )
hi,
me new to genomics.
I handle critical SNPs in the promoter region of certain genes and assess their significance by gene expression studies.
i get the possible SNPs on the 5'UTR region of the gene from dbSNP but i dont understand how to get the exact base location of the SNP
from the site of initiation of transcription.
ie distance (bp) to major transcription initiation site of the gene.
how can i get this distance data.
any comments would be greatly helpful.
Hi,
First, you can check genome databases such as ensembl.org to find out the predicted start site of transcription or the first exon. To make sure the prediction is accurate, at the mean time, you can also check Genbank sequences for that gene and publications to find out whether experimentally determined transcriptional start site matches predicted one. So you must do some database searches before you can find what you want.
First, you can check genome databases such as ensembl.org to find out the predicted start site of transcription or the first exon. To make sure the prediction is accurate, at the mean time, you can also check Genbank sequences for that gene and publications to find out whether experimentally determined transcriptional start site matches predicted one. So you must do some database searches before you can find what you want.
Ok. Thx so much
Try using the SNPper database they provide those data, I think you can choose between position from translation start site and transcription start site.
http://snpper.chip.org/
you'll have to registre but everything is free.
I love this site!!!