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Annotation Attributes

Annotation Attributes

A standard set of attributes with strictly defined meanings are being added to the Vega annotation. Where present these are shown on Gene Summary and Transcript Summary Panels.

Transcript level attributes

transcript contains two confidently annotated CDSs. Support may come from eg proteomic data, cross-species conservation or published experimental work
ranscript 5' end overlaps ENCODE or Fantom CAGE cluster
dotter confirmed
transcript QC checked using dotplot to identify features eg splice junctions, end of homology
inferred exon combination
transcript model is not supported by any publicly available transcript evidence; may be supported by eg published experimental data
inferred transcript model
transcript model is not supported by a single piece of transcript evidence; may be supported by multiple fragments of transcript evidence or by combining different evidence sources eg protein homology, RNAseq data, published experimental data
low sequence quality
transcript supported by transcript evidence that, while mapping best-in-genome, shows regions of poor sequence quality
non-submitted evidence
transcript supported by sequence evidence from as yet unpublished experimental study
transcript connecting two independent loci i.e. transcript has exons that overlap exons from transcripts belonging to 2 or more different loci (in addition to the locus to which the readthrough transcript itself belongs)
retained intron CDS
internal intron of CDS portion of transcript is retained
retained intron final
final intron of CDS portion of transcript is retained
retained intron first
first intron of CDS portion of transcript is retained
RNA-Seq supported only
transcript either supported in full by RNAseq data or has unique splice feature that is only supported by RNAseq data
RP supported TIS
transcript contains a CDS that has a translation initiation site supported by Ribosomal Profiling data
translation of the functional protein due to eg experimental evidence, poor cross-species conservation, weak Kozak context, interference with signal peptides or targeting signals

Gene level attributes

fragmented locus
locus is not completely spanned by transcript evidence and the overlaps between all transcripts at the locus cannot be determined
protein-coding locus with no paralogs or ortholgs
overlapping locus
locus overlapped by at least one transcript belonging to another locus
reference genome error
locus overlaps a sequence error in the reference genome that affects its annotation
protein-coding locus created via retrotransposition