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Vega gene and transcript types

Vega shows annotation from different sources and classifies genes and transcripts into different classes. Since a single gene often has more than one transcript, and these transcripts can be of different classes, the classification of the gene as a whole is defined by the transcipt with the 'highest' level of classification.

Annotation sources

There are four distinct sets of sources for the annotation of genes and transcripts in Vega. These are shown as different tracks and have different colour schemes.

  • Havana Core Genes have been annotated in depth to identify alternative transcripts, and are present for all species. They have been annotated by the Havana group at the WTSI.
  • Havana Update Genes represent updates to annotation that have been made since the Core gene set was made. They have been annotated to the same extent as the core genes but are not incorporated into the website to the same extent. They are currently present for human only.
  • LoF genes show the consequences of variations in sequence on the functional properties of human transcripts.
  • KO genes are artificial mouse genes identified by Havana as part of the EUCOMM and KOMP gene targetting projects. The gene structures shown are the result of knocking out the critical exons, ie the exon(s) required for the correct translation of the longest transcript.

For each of these sets, genes and transcripts are classified as shown below. The exception to this are the KO genes, which being artificial are not given a gene type.

Gene Classification

Genes can be classified according to their status, which indicates the type of evidence that supports the annotation, and their biotype, an indicator of biological significance. For simplicity of display, genes are coloured according to their biotype only, so for example 'Known Protein coding' and 'Novel Protein coding' genes are both shown in the same shade of blue.

Status:

  • Known. Identical to known cDNAs or proteins from the same species and has an entry in species specific model databases: EntrezGene for human dog and pig, MGI for mouse, and Zfin for Zebrafish.
  • Novel. Identical or homologous to cDNAs from the same species, or proteins from all species.
  • Putative. Identical or homologous to spliced ESTs from the same species.
  • Predicted. Based on ab initio prediction and for which at least one exon is supported by biological data (unspliced ESTs, protein sequence similarity with mouse or tetraodon genomes or expression data from Rosetta).
  • Genes may have no status shown where this is not applicable, as for example with the majority of pseudogenes.

Biotype:

  • Protein coding. Contains an open reading frame (ORF).
    • Polymorphic. A protein coding gene that has at least one transcript with a valid ORF and one or more coding transcripts that contain a polymorphism.
  • Processed transcripts. Doesn't contain an ORF. Divided into three major categories.
    • Long non-coding RNA (lncRNA). Subclassified into one of the following types:
      • Non coding. Contains transcripts which are known from the literature to not be protein coding.
      • 3prime_overlapping_ncrna. Has transcripts where ditag and/or published experimental data strongly supports the existence of long (>200bp) non-coding transcripts that overlap the 3'UTR of a protein-coding locus on the same strand.
      • Ambiguous_orf. Has transcripts that are believed to be protein coding, but have more than one possible open reading frame.
      • Antisense. Has transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand.
      • lincRNA (long interspersed ncRNA). Has transcripts that are long intergenic non-coding RNA locus with a length >200bp. Requires lack of coding potential and may not be conserved between species.
      • ncRNA_host. Has a separate non-coding transcript that hosts non-coding microRNAs such as like MIRs.
      • Retained_intron. Has an alternatively spliced transcript believed to contain intronic sequence relative to other, coding, variants.
      • Sense_intronic. Has a long non-coding transcript in introns of a coding gene that does not overlap any exons.
      • Sense_overlapping. Has a long non-coding transcript that contains a coding gene in its intron on the same strand.
      • macro_lncRNA. unspliced lncRNAs that are several kb in size.
    • ncRNA
      • miRNA. microRNA
      • piRNA. piwi-interacting RNA
      • rRNA. ribsosomal RNA
      • siRNA. small interfering RNA
      • snRNA. small nuclear RNA
      • snoRNA. small nucleolar RNA
      • tRNA. transfer RNA
      • vaultRNA. Short non coding RNA genes that form part of the vault ribonucleoprotein complex.
    • Unclassified processed transcript. Cannot be placed in one of the other categories.
  • Pseudogene. Similar to known proteins but contain a frameshift and/or stop codon(s) which disrupts the ORF. These can be classified into the following:
    • Processed pseudogene. Pseudogene that lack introns and is thought to arise from reverse transcription of mRNA followed by reinsertion of DNA into the genome.
    • Unprocessed pseudogene. Pseudogene that can contain introns since produced by gene duplication.
    • Transcribed pseudogene. Pseudogene where protein homology or genomic structure indicates a pseudogene, but the presence of locus-specific transcripts indicates expression. These can be classified into 'Processed', 'Unprocessed' and 'Unitary'.
    • Translated pseudogene. Pseudogenes that have mass spec data suggesting that they are also translated. These can be classified into 'Processed', 'Unprocessed'
    • Polymorphic pseudogene. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
    • Unitary pseudogene. A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.
    • IG Pseudogene. Inactivated immunoglobulin gene.
  • IG Gene. Immunoglobulin gene.
  • TR Gene. T cell receptor gene.
  • TEC (To be Experimentally Confirmed). This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.

Transcript Classification

Transcripts are classified according to their class.

  • Protein coding. Protein coding transcripts. These can be further classified as follows:
    • Known Protein coding. 100% Identical to RefSeq NP or Swiss-Prot entry.
    • Novel Protein coding. Shares >60% length with known coding sequence from RefSeq or Swiss-Prot or has cross-species/family support or domain evidence.
    • Putative Protein coding. Shares <60% length with known coding sequence from RefSeq or Swiss-Prot, or has an alternative first or last coding exon.
    • Nonsense mediated decay. If the coding sequence (following the appropriate reference) of a transcript finishes >50bp from a downstream splice site then it is tagged as NMD. If the variant does not cover the full reference coding sequence then it is annotated as NMD if NMD is unavoidable i.e. no matter what the exon structure of the missing portion is the transcript will be subject to NMD.
    • Nonstop decay. Transcripts that have polyA features (including signal) without a prior stop codon in the CDS, i.e. a non-genomic polyA tail attached directly to the CDS without 3' UTR. These transcripts are subject to degradation.
  • Processed transcripts. Doesn't contain an ORF. Divided into three major categories.
    • Long non-coding RNA (lncRNA). Subclassified into one of the following types:
      • Non coding. Contains transcripts which are known from the literature to not be protein coding.
      • 3prime_overlapping_ncrna. Has transcripts where ditag and/or published experimental data strongly supports the existence of long (>200bp) non-coding transcripts that overlap the 3'UTR of a protein-coding locus on the same strand.
      • Ambiguous_orf. Has transcripts that are believed to be protein coding, but have more than one possible open reading frame.
      • Antisense. Has transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand.
      • lincRNA (long interspersed ncRNA). Has transcripts that are long intergenic non-coding RNA locus with a length >200bp. Requires lack of coding potential and may not be conserved between species.
      • ncRNA_host. Has a separate non-coding transcript that hosts non-coding microRNAs such as like MIRs.
      • Retained_intron. Has an alternatively spliced transcript believed to contain intronic sequence relative to other, coding, variants.
      • Sense_intronic. Has a long non-coding transcript in introns of a coding gene that does not overlap any exons.
      • Sense_overlapping. Has a long non-coding transcript that contains a coding gene in its intron on the same strand.
      • macro_lncRNA. unspliced lncRNAs that are several kb in size.
    • ncRNA
      • miRNA. microRNA
      • piRNA. piwi-interacting RNA
      • rRNA. ribsosomal RNA
      • siRNA. small interfering RNA
      • snRNA. small nuclear RNA
      • snoRNA. small nucleolar RNA
      • tRNA. transfer RNA
      • vaultRNA. Short non coding RNA genes that form part of the vault ribonucleoprotein complex.
    • Unclassified processed transcript. Cannot be placed in one of the other categories.
  • Pseudogene. Have homology to proteins but generally suffer from a disrupted coding sequence and an active homologous gene can be found at another locus. Sometimes these entries have an intact coding sequence or an open but truncated ORF, in which case there is other evidence used (for example genomic polyA stretches at the 3' end) to classify them as a pseudogene. Can be further classified as follows:
    • Processed pseudogene. Pseudogene that appears to have been produced by integration of a reverse transcribed mRNA into the genome.
    • Unprocessed pseudogene. Pseudogene that shows evidence of loss of function, but has exon-intron structure.
    • Transcribed pseudogene. Pseudogene where protein homology or genomic structure indicates a pseudogene, but the presence of locus-specific transcripts indicates expression. These can be classified into 'Processed' and 'Unprocessed'.
    • Translated pseudogene. Pseudogenes that have mass spec data suggesting that they are also translated. These can be classified into 'Processed' and 'Unprocessed'
    • Polymorphic pseudogene. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
    • Unitary pseudogene. A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.
    • IG Pseudogene. Inactivated immunoglobulin gene.
  • TEC (To be Experimentally Confirmed). This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of novel protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.
  • Artifact. Used to tag mistakes in the public databases (Ensembl/SwissProt/ Trembl). Usually these arise from high-throughput cDNA sequencing projects, which submit automatic annotation sometimes resulting in erroneous coding sequences that are, for example, 3' UTRs.
  • IG Gene. Immunoglobulin gene.
  • TR Gene. T cell receptor gene.
  • Disrupted domain. Otherwise viable coding region omitted from this alternatively spliced transcript because the splice variation affects a region coding for a protein domain.