How to find the gene structure of a gene?

Question

[Dayna]

Hi all

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

Thank you

[Pierre Lindenbaum]

... what have you found so far ?

[shawn.w.foley]

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?

[Dayna]

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

Answer 1

[Alex Reynolds]

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

Answer 2

[sacha]

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

Answer 3

[Emily]

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.

Answer 4

[Emily]

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.

[Dayna]

Thanks Emily_Ensemble :)