Class SpliceSite

All Implemented Interfaces:
Serializable, Cloneable, 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:
  • Field Details

    • CORE_SPLICE_SITE_SIZE

      public static final int CORE_SPLICE_SITE_SIZE
      See Also:
    • SPLICE_REGION_EXON_SIZE

      public static final int SPLICE_REGION_EXON_SIZE
      See Also:
    • SPLICE_REGION_INTRON_MIN

      public static final int SPLICE_REGION_INTRON_MIN
      See Also:
    • SPLICE_REGION_INTRON_MAX

      public static final int SPLICE_REGION_INTRON_MAX
      See Also:
  • Constructor Details

    • SpliceSite

      public SpliceSite()
    • SpliceSite

      public SpliceSite(Exon parent, int start, int end, boolean strandMinus, String id)
    • SpliceSite

      public SpliceSite(Intron parent, int start, int end, boolean strandMinus, String id)
  • Method Details

    • 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
    • variantEffect

      public boolean variantEffect(Variant variant, VariantEffects variantEffects)
      Description copied from class: Marker
      Calculate the effect of this variant
      Overrides:
      variantEffect in class Marker