Package org.snpeff.interval

Class SpliceSite

java.lang.Object

org.snpeff.interval.Interval

org.snpeff.interval.Marker

org.snpeff.interval.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

Field Summary

Fields

Modifier and Type	Field	Description
static int	CORE_SPLICE_SITE_SIZE
static int	SPLICE_REGION_EXON_SIZE
static int	SPLICE_REGION_INTRON_MAX
static int	SPLICE_REGION_INTRON_MIN

Fields inherited from class org.snpeff.interval.Marker

type

Fields inherited from class org.snpeff.interval.Interval

chromosomeNameOri, end, id, parent, start, strandMinus

Constructor Summary

Constructors

Constructor	Description
SpliceSite()
SpliceSite(Exon parent, int start, int end, boolean strandMinus, java.lang.String id)
SpliceSite(Intron parent, int start, int end, boolean strandMinus, java.lang.String id)

Method Summary

Modifier and Type	Method	Description
abstract boolean	intersectsCoreSpliceSite(Marker marker)	Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.
protected boolean	isShowWarningIfParentDoesNotInclude()	Splice sites are not included in Exons, by definition.
boolean	variantEffect(Variant variant, VariantEffects variantEffects)	Calculate the effect of this variant

Methods inherited from class org.snpeff.interval.Marker

adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, toString, union, variantEffectNonRef

Methods inherited from class org.snpeff.interval.Interval

equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

CORE_SPLICE_SITE_SIZE

public static final int CORE_SPLICE_SITE_SIZE

See Also:

Constant Field Values

SPLICE_REGION_EXON_SIZE

public static final int SPLICE_REGION_EXON_SIZE

See Also:

Constant Field Values

SPLICE_REGION_INTRON_MIN

public static final int SPLICE_REGION_INTRON_MIN

See Also:

Constant Field Values

SPLICE_REGION_INTRON_MAX

public static final int SPLICE_REGION_INTRON_MAX

See Also:

Constant Field Values

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

variantEffect

public boolean variantEffect(Variant variant,
                             VariantEffects variantEffects)

Description copied from class: Marker

Calculate the effect of this variant

Overrides:

variantEffect in class Marker