Question: How to get the coding sequence of each isoform of a gene?
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gravatar for bounlu
3.9 years ago by
bounlu170
Singapore
bounlu170 wrote:

I want to know if my siRNA sequence is present in all the isoforms of my gene to make sure that it targets and knock outs my gene for all possible isoforms. For this, I need the coding nucleotide sequence of each isoform to do the intersection. CCDS gives only the consensus sequence, UCSC is not straightforward to get what I want, so I am looking for an elegant way of doing this. Any idea?

isoform sequence • 2.0k views
ADD COMMENTlink modified 3.9 years ago by Emily_Ensembl18k • written 3.9 years ago by bounlu170
2
gravatar for Emily_Ensembl
3.9 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

You could look at the transcript comparison view in Ensembl.

ADD COMMENTlink written 3.9 years ago by Emily_Ensembl18k
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gravatar for pld
3.9 years ago by
pld4.8k
United States
pld4.8k wrote:

Ensembl does a good job of organizing isoforms:

http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000109971;r=11:123057489-123063230;redirect=no

For each gene you can look at the transcript table and it will list all of the isoforms. You might be able to automate this through biomart.

 

ADD COMMENTlink written 3.9 years ago by pld4.8k
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