alternative splicing in fasta format
Hi all,
I need to download all those genes for homo sapiens that present alternative splicing. I need these files in fasta format and separately based on their types of alternative splicing (Cassette exon, Intron retention, Mutually exclusive exons, Alternative 3' sites, Alternative 5' sites, Alternative first exon, Alternative last exon.)
Would you please tell me from which database I can do that? I saw Ensembl but I don't know how extract the files.
Thank you for your attention.
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What you probably need is not gene, but transcript fasta as one gene can have multiple alternative transcripts that originate trough different splicing mechanisms (alternative 3' sites, alternative 5' sites, etc).
Would you please tell me from which database I can do that?
You can read this document, might be helpful. It contains a list of Alternative Splicing databases, you can have a look at them and decide which one serves your purpose.
From Ensembl, like you say.
The file, that you linked, contains the following transcript types:
Can you tell me how to interpret which ones are cassette exons, mutually exclusive exons, and the other splice types that the OP has asked?