alternative splicing in fasta format

Question

[sentinel]

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.

[PoGibas]

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).

[sentinel]

Would you please tell me from which database I can do that?

[Emily]

From Ensembl, like you say.

[komal.rathi]

The file, that you linked, contains the following transcript types:

antisense
IG_C_gene
IG_C_pseudogene
IG_D_gene
IG_J_gene
IG_J_pseudogene
IG_V_gene
IG_V_pseudogene
lincRNA
misc_RNA
nonsense_mediated_decay
non_stop_decay
polymorphic_pseudogene
processed_pseudogene
processed_transcript
protein_coding
pseudogene
retained_intron
sense_overlapping
TEC
transcribed_processed_pseudogene
transcribed_unitary_pseudogene
transcribed_unprocessed_pseudogene
translated_processed_pseudogene
translated_unprocessed_pseudogene
TR_C_gene
TR_D_gene
TR_J_gene
TR_J_pseudogene
TR_V_gene
TR_V_pseudogene
unitary_pseudogene
unprocessed_pseudogene

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?

[komal.rathi]

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.