Question: How to find the gene structure of a gene?
0
gravatar for Dayna
3.1 years ago by
Dayna20
Dayna20 wrote:

Hi all

Does anyone know a tool to find the gene structure of a gene?

Thank you

gene structure • 837 views
ADD COMMENTlink modified 3.1 years ago by Emily_Ensembl21k • written 3.1 years ago by Dayna20
1

... what have you found so far ?

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum134k
1

Can you give more detail about what you're looking for? Are you annotating genes de novo and trying to predict structure? Does structure mean where is the CDS? Are you interested in each exon, and each UTR? Is this a novel organism or are you looking for annotation files?

ADD REPLYlink written 3.1 years ago by shawn.w.foley1.2k

I need to check a variant. so i want to take a look generally to the gene of it

ADD REPLYlink written 3.1 years ago by Dayna20
1
gravatar for Alex Reynolds
3.1 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

Search for your gene of interest in the UCSC Genome Browser, or similar.

ADD COMMENTlink written 3.1 years ago by Alex Reynolds31k
1
gravatar for sacha
3.1 years ago by
sacha2.1k
France
sacha2.1k wrote:

RefGene: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz

ADD COMMENTlink written 3.1 years ago by sacha2.1k
1
gravatar for Emily_Ensembl
3.1 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

If you want to look at a variant in terms of genes, your best start point is to run it through the VEP. You'll get the effect and the position of the variant in the gene, and you can click through to view the gene structure and sequence.

ADD COMMENTlink written 3.1 years ago by Emily_Ensembl21k
1
gravatar for Emily_Ensembl
3.1 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

If you want to look at a variant in terms of genes, your best start point is to run it through the VEP. You'll get the effect and the position of the variant in the gene, and you can click through to view the gene structure and sequence.

ADD COMMENTlink written 3.1 years ago by Emily_Ensembl21k

Thanks Emily_Ensemble :)

ADD REPLYlink written 3.1 years ago by Dayna20
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