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.
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2 replies to this topic
#2
pcrman
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Posted 02 January 2005 - 02:25 PM
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.
#3
rajgene
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Posted 03 January 2005 - 12:51 AM
pcrman, on Jan 2 2005, 03:25 PM, said:
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.
