class |
Cds |
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is
that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
|
class |
Chromosome |
Interval for the whole chromosome
If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
|
class |
Custom |
This is a custom interval (i.e.
|
class |
Downstream |
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
|
class |
Exon |
Interval for an exon
|
class |
Gene |
Interval for a gene, as well as transcripts
|
class |
GenericMarker |
An interval intended as a mark
|
class |
Genome |
This is just used for the Interval class.
|
class |
GffMarker |
An interval intended as a mark
|
class |
Gtf2Marker |
An interval intended as a mark
|
class |
Intergenic |
Interval for in intergenic region
|
class |
IntergenicConserved |
Interval for a conserved intergenic region
|
class |
IntervalAndSubIntervals<T extends Marker> |
Interval that contains sub intervals.
|
class |
Intron |
Intron
|
class |
IntronConserved |
Interval for a conserved non-coding region in an intron
|
class |
Marker |
An interval intended as a mark
|
class |
MarkerParentId |
This is a marker used as a 'fake' parent during data serialization
|
class |
MarkerSeq |
Marker with a DNA sequence
|
class |
MicroRnaBindingSite |
miRna binding site (usually this was predicted by some algorithm)
|
class |
Motif |
Regulatory elements
|
class |
NextProt |
NextProt annotation marker
|
class |
ProteinInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid.
|
class |
ProteinProteinInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid
within the same protein.
|
class |
ProteinStructuralInteractionLocus |
Protein interaction: An amino acid that is "in contact" with another amino acid.
|
class |
RareAminoAcid |
Rare amino acid annotation:
These are amino acids that occurs very rarely in an organism.
|
class |
Regulation |
Regulatory elements
|
class |
SpliceSite |
Interval for a splice site
Reference: http://en.wikipedia.org/wiki/RNA_splicing
Spliceosomal introns often reside in eukaryotic protein-coding genes.
|
class |
SpliceSiteAcceptor |
Interval for a splice site acceptor
Note: Splice sites donnor are defined as the last 2 bases of an intron
Reference: http://en.wikipedia.org/wiki/RNA_splicing
|
class |
SpliceSiteBranch |
A (putative) branch site.
|
class |
SpliceSiteBranchU12 |
A (putative) U12 branch site.
|
class |
SpliceSiteDonor |
Interval for a splice site donnor
Note: Splice sites donnor are defined as the first 2 bases of an intron
Reference: http://en.wikipedia.org/wiki/RNA_splicing
|
class |
SpliceSiteRegion |
Interval for a splice site acceptor
From Sequence Ontology: A sequence variant in which a change has occurred
within the region of the splice site, either within 1-3 bases of the exon
or 3-8 bases of the intron.
|
class |
Transcript |
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
|
class |
Upstream |
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
|
class |
Utr |
Interval for a UTR (5 prime UTR and 3 prime UTR
|
class |
Utr3prime |
Interval for a UTR (5 prime UTR and 3 prime UTR
|
class |
Utr5prime |
Interval for a UTR (5 prime UTR and 3 prime UTR
|
class |
Variant |
A variant represents a change in a reference sequence
Notes:
This class was previously known as Variant.
|
class |
VariantBnd |
A 'BND' variant (i.e.
|
class |
VariantNonRef |
A variant respect to non-reference (e.g.
|
class |
VariantWithScore |
A variant that has a numeric score.
|