extract isoform sequences of splicing variants?

Question

[biocyberman]

Say I have this splicing variant (isoform): r.4357_4358ins4358-2785_4358-2719 And I have gene name BRCA1, and if necessary, reference transcript: https://www.ncbi.nlm.nih.gov/nuccore/NM_007294.3

What is the convenient way to get mRNA sequence of the isoform?

Update:

Would like to mention that I can download all known isoforms like this: https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000012048;r=17:43044295-43170245 But I am more interested in something that can parse isoform names and extract sequences on the fly.

[caggtaagtat]

You can look it up in ensembl.org. Search for BRCA1, than go to the transcirpt table and look for "NM_007294.3" in the RefSeq column. Than you select the respective transcript and go to "Exons" on the left table.

Now you should see the Sequenz if you scroll down. You can also download it.

Here is the link. I hope its the right one :)

Edit: Sorry, I just told you to find the sequence of your reference, which you already have...

Answer 1

[EagleEye]

To get mRNA sequence of any transcript variant of particular gene:

1. Go to UCSC table browser (I assume you are looking for Human data)
2. Set following parameters: group: Genes and Gene predictions
3. In identifiers (names/accessions): click 'paste list' and enter 'BRCA1' in the text box and submit
4. output format: Choose 'Sequence'
5. Click 'get output' button
6. Next screen select mRNA -> submit

Now you will get mRNA sequence for all transcript variants of BRCA1.

I hope this is what you are looking for.

[biocyberman]

This would do for known isoforms in UCSC. I was thinking about something that can parse the isoform name (e.g. r.4357_4358ins4358-2785_4358-2719) and generate the sequence on the fly.

[EagleEye]

From where did you get this name "r.4357_4358ins4358-2785_4358-2719" ? source !!!