Bio::SeqFeature::Gene::Intron(3) An intron feature

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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AUTHOR - David Block

Email [email protected]

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

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