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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