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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME Bio::EnsEMBL::Intron - A class representing an Intron

SYNOPSIS

$intron = Bio::EnsEMBL::Intron->new( exon1, exon2, $analysis );

new

Arg [1]    : Bio::EnsEMBL::Exon The 5' exon for the intron; required
Arg [2]    : Bio::EnsEMBL::Exon The 3' exon for the intron; required
Arg [3]    : Bio::EnsEMBL::Analysis Analysis to link to this Intron
Example    : $intron = new Bio::EnsEMBL::Intron($exon1, $exon2)
Description: Create an Intron object from two exons and an optional analysis
Returntype : Bio::EnsEMBL::Intron
Exceptions : exons not on the same strand or slice.
Caller     : general
Status     : Stable

length

Args       : none
Example    : $length = $intron->length();
Description: Returns the length of this intron
Returntype : Integer
Exceptions : none
Caller     : general
Status     : Stable

prev_Exon

Args       : none
Example    : $exon = $intron->prev_Exon
Description: Returns the exon before this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller     : general
Status     : Stable

next_Exon

Args       : none
Example    : $exon = $intron->next_Exon
Description: Returns the exon after this Intron
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller     : general
Status     : Stable

rank

Args       : none
Example    : $rank = $intron->rank
Description: Returns the rank of this Intron
Returntype : Integer
Exceptions : none
Caller     : general
Status     : Stable

is_splice_canonical

Example     : my $canonical = $intron->is_splice_canonical(); 
Description : Indicates if the splice site is considered normal. This means
              splice site variants equal to (D == donor, A == acceptor)
                GT (D) => AG (A) 
                AT (D) => AC (A)
                GC (D) => AG (A)
Returntype  : Boolean indicating if the splice was as expected
Exceptions  : See splice_seq

splice_seq

Example     : my ($donor, $acceptor) = @{$intron->splice_seq}; 
Description : Get the donor and acceptor splice sites for this intron
Returntype  : ArrayRef[String] The donor and acceptor sequences as Strings
Exceptions  : Thrown if a feature Slice cannot be found