Package org.snpeff.interval
Class SpliceSite
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.SpliceSite
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,TxtSerializable
- Direct Known Subclasses:
SpliceSiteAcceptor
,SpliceSiteBranch
,SpliceSiteDonor
,SpliceSiteRegion
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:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionSpliceSite
(Exon parent, int start, int end, boolean strandMinus, String id) SpliceSite
(Intron parent, int start, int end, boolean strandMinus, String id) -
Method Summary
Modifier and TypeMethodDescriptionabstract boolean
intersectsCoreSpliceSite
(Marker marker) Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins.protected boolean
Splice sites are not included in Exons, by definition.boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantMethods 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
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Field Details
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CORE_SPLICE_SITE_SIZE
public static final int CORE_SPLICE_SITE_SIZE- See Also:
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SPLICE_REGION_EXON_SIZE
public static final int SPLICE_REGION_EXON_SIZE- See Also:
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SPLICE_REGION_INTRON_MIN
public static final int SPLICE_REGION_INTRON_MIN- See Also:
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SPLICE_REGION_INTRON_MAX
public static final int SPLICE_REGION_INTRON_MAX- See Also:
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Constructor Details
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SpliceSite
public SpliceSite() -
SpliceSite
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SpliceSite
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Method Details
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intersectsCoreSpliceSite
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 classMarker
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variantEffect
Description copied from class:Marker
Calculate the effect of this variant- Overrides:
variantEffect
in classMarker
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