Bio::SeqFeature::Gene::Intron - DESCRIPTION of Object Give standard usage here Describe the object here

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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