Question: RNA Splicing databases
2
gravatar for ga87mit
8 weeks ago by
ga87mit20
ga87mit20 wrote:

Hello, I'm working on predicting RNA splicing. What are good databases that contain RNA sequences and their splicing sites?

ADD COMMENTlink modified 8 weeks ago by Geparada1.4k • written 8 weeks ago by ga87mit20
1
gravatar for Geparada
8 weeks ago by
Geparada1.4k
Cambridge
Geparada1.4k wrote:

In general you can find the splice sites from gene models such as GENCODE (https://www.gencodegenes.org/), refseq or UCSC genes. I particularly recommend you to use GENCODE since is constantly getting improved. You can extract splicing sites from GTF, GFF or bed12 files. If you use UCSC Table Browser you can access to a different "gene and genes predictions" files and choose the format that is easier to you to understand. Now, if you are interested in alternative splicing I would recommend VastDB (http://vastdb.crg.eu/wiki/Main_Page).

I hope this helps, Cheers

ADD COMMENTlink written 8 weeks ago by Geparada1.4k
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