RNA Splicing databases
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3.7 years ago
ga87mit ▴ 20

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

sequence RNA-Seq splicing database • 1.3k views
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3.7 years ago
Geparada ★ 1.5k

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

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