NAME

       Bio::SeqFeature::Gene::Intron - An intron feature

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here

FEEDBACK

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       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
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   Support
       Please direct usage questions or support issues to the mailing list:

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       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

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AUTHOR - David Block

       Email dblock@gene.pbi.nrc.ca

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   upstream_Exon
         Title   : upstream_Exon
         Usage   : $intron->upstream_Exon()
         Function: exon upstream of the intron
         Returns : Bio::EnsEMBL::Exon
         Args    :

   downstream_Exon
         Title   : downstream_Exon
         Usage   : $intron->downstream_Exon()
         Function: exon downstream of the intron
         Returns : Bio::EnsEMBL::Exon
         Args    :

   phase
         Title   : phase
         Usage   : $intron->phase()
         Function: returns the phase of the intron(where it interrupts the codon)
         Returns : int(0,1,2)
         Args    :

   acceptor_splice_site
         Title   : acceptor_splice_site
         Usage   : $intron->acceptor_splice_site(21,3)
         Function: returns the sequence corresponding to the
                   consensus acceptor splice site. If start and
                   end are provided, it will number of base pairs
                   left and right of the canonical AG. Here 21 means
                   21 bp into intron and 3 means 3 bp into the exon.
                   --Intron--21----|AG|-3-----Exon
                   Defaults to 21,3

         Returns : Bio::Seq
         Args    : start and end

   donor_splice_site
         Title   : donor_splice_site
         Usage   : $intron->donor_splice_site(3,6)
         Function: returns the sequence corresponding to the
                   consensus donor splice site. If start and
                   end are provided, it will number of base pairs
                   left and right of the canonical GT. Here 3 means
                   3 bp into exon and 6 means 6 bp into the intron.
                   --Exon-3--|GT|-6----Intron-
                   Defaults to 3,6

         Returns : Bio::Seq
         Args    : start and end