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  • efoss
    Member
    • Jul 2011
    • 98

    #1

    looking for file with known human splice donor and acceptor sites

    I am trying to find a file I can download with all known human splice donor and acceptor sites. The donor and acceptor sites don't need to be paired, i.e. it's not important that the file specifies that donor site X is hooked up with acceptor site Y. I've been looking around in the "Tables" section of the UCSC Genome browser site but not finding anything (though there is so much there that I could easily be missing stuff). Does anyone know where I can find a file like this, or can people steer me in the right direction to find such a file (or a related file that I can parse to get what I want)?

    Thank you.

    Eric
  • Simon Anders
    Senior Member
    • Feb 2010
    • 995

    #2
    Why don't you simply use a GTF gene annotation file such as this one? You simply use the boundaries of all the exons, and once you take care of removing the 5' ends of first exons and the 5' ends of last exons, you have a long list of splice sites.

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    • efoss
      Member
      • Jul 2011
      • 98

      #3
      Originally posted by Simon Anders View Post
      Why don't you simply use a GTF gene annotation file such as this one? You simply use the boundaries of all the exons, and once you take care of removing the 5' ends of first exons and the 5' ends of last exons, you have a long list of splice sites.
      Perfect! Thanks so much.

      Eric

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