Annotation Attributes

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

Transcript level attributes

bicistronic

transcript contains two confidently annotated CDSs. Support may come from e.g. proteomic data, cross-species conservation or published experimental work

CAGE supported TSS

transcript 5' end overlaps ENCODE or Fantom CAGE cluster

dotter confirmed

transcript checked using DOTTER dotplot alignment of homology evidence to genomic sequence to confirm exon structure

inferred exon combination

transcript model contains all possible in-frame exons supported by homology, experimental evidence or conservation, but the exon combination is not directly supported by a single piece of evidence and may not be biological. Used for large genes with repetitive exons (e.g. titin (TTN)) to represent all the exons individual transcript variants can pool from

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 e.g. protein homology, RNA-seq data, published experimental data

low sequence quality

transcript supported by transcript evidence that, while mapping best-in-genome, shows regions of poor sequence quality

not organism-supported

mRNA, EST or protein homology evidence from orthologous loci from other species can be used to build variants on the condition that the homology is perfectly co-linear and all normal splicing rules are upheld

non-submitted evidence

transcript supported by sequence evidence from as yet unpublished experimental study

readthrough

transcript connecting two independent loci, i.e. transcript has exons that overlap exons from transcripts belonging to 2 or more different loci

retained intron CDS

CDS codes through an internal retained intron (compared to a reference variant)

retained intron final

CDS ends in, or downstream of, a retained intron that, compared to a reference variant, is immediately downstream of the last coding exon

retained intron first

CDS starts in, or upstream of, a retained intron that, compared to a reference variant, is immediately upstream of the first coding exon

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

upstream ATG

an upstream ATG exists, but the ATG for the current CDS has been chosen taking into account factors like cross-species conservation, strength of Kozak sequence, signal peptides, experimental evidence, and ribosome profiling

3' nested supported extension

3' end extended based on RNA-seq data

3' standard supported extension

3' end extended based on RNA-seq data

454 RNA-Seq supported

annotated based on RNA-seq data

5' nested supported extension

5' end extended based on RNA-seq data

5' standard supported extension

5' end extended based on RNA-seq data

RNA-Seq supported only

annotated based on RNA-seq data

RNA-Seq supported partial

annotated based on mixture of RNA-seq data and EST/mRNA/protein evidence

nested 454 RNA-Seq supported

annotated based on RNA-seq data

Gene level attributes

fragmented locus

locus consists of non-overlapping transcript fragments either because of genome assembly issues (i.e., gaps or mis-assemblies), or because supporting transcripts (e.g., from another species) cannot be completely mapped, or because the supporting transcripts are non-overlapping end pairs (i.e., 5' and 3' ESTs from a single cDNA)

orphan

protein-coding locus with no paralogues or orthologs

overlapping locus

exon(s) of the locus overlap exon(s) of a readthrough transcript or a transcript belonging to another locus

reference genome error

locus overlaps a sequence error or an assembly error in the reference genome that affects its annotation (e.g., 1 or 2bp insertion/deletion, substitution causing premature stop codon). The main effect is that affected transcripts that would have had a CDS are currently annotated without one

retrogene

protein-coding locus created via retrotransposition

ncRNA host

locus is host to ncRNAs such as piRNA, miRNA, snoRNA, etc.