Class SpliceSite

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, TxtSerializable
    Direct Known Subclasses:
    SpliceSiteAcceptor, SpliceSiteBranch, SpliceSiteDonor, SpliceSiteRegion

    public abstract class SpliceSite
    extends Marker
    Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes. Within the intron, a 3' splice site, 5' splice site, and branch site are required for splicing. The 5' splice site or splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved consensus region. The 3' splice site or splice acceptor site terminates the intron with an almost invariant AG sequence. Upstream (5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Upstream from the polypyrimidine tract is the branch point, which includes an adenine nucleotide.
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • SpliceSite

        public SpliceSite()
      • SpliceSite

        public SpliceSite​(Exon parent,
                          int start,
                          int end,
                          boolean strandMinus,
                          java.lang.String id)
      • SpliceSite

        public SpliceSite​(Intron parent,
                          int start,
                          int end,
                          boolean strandMinus,
                          java.lang.String id)
    • Method Detail

      • intersectsCoreSpliceSite

        public abstract boolean intersectsCoreSpliceSite​(Marker marker)
        Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins. Usually CORE_SPLICE_SITE_SIZE is 2 bases. Other spice sites are considered "non-core".
      • isShowWarningIfParentDoesNotInclude

        protected boolean isShowWarningIfParentDoesNotInclude()
        Splice sites are not included in Exons, by definition.
        Overrides:
        isShowWarningIfParentDoesNotInclude in class Marker