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?
2 answers
You could look at the transcript comparison view in Ensembl.
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.
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