Gene/Transcript Biotypes in GENCODE & Ensembl

Please also compare to the VEGA descriptions.

Further details about the annotation of non-coding RNAs are listed on this Ensembl page.

Biotype	Definition
IG_C_gene IG_D_gene IG_J_gene IG_LV_gene IG_V_gene TR_C_gene TR_J_gene TR_V_gene TR_D_gene	Immunoglobulin (Ig) variable chain and T-cell receptor (TcR) genes imported or annotated according to the IMGT.
IG_pseudogene IG_C_pseudogene IG_J_pseudogene IG_V_pseudogene TR_V_pseudogene TR_J_pseudogene	Inactivated immunoglobulin gene.
Mt_rRNA Mt_tRNA miRNA misc_RNA rRNA scRNA snRNA snoRNA ribozyme sRNA scaRNA	Non-coding RNA predicted using sequences from Rfam and miRBase
lncRNA	Generic long non-coding RNA biotype that replaced the following biotypes: 3prime_overlapping_ncRNA, antisense, bidirectional_promoter_lncRNA, lincRNA, macro_lncRNA, non_coding, processed_transcript, sense_intronic and sense_overlapping.
Mt_tRNA_pseudogene tRNA_pseudogene snoRNA_pseudogene snRNA_pseudogene scRNA_pseudogene rRNA_pseudogene misc_RNA_pseudogene miRNA_pseudogene	Non-coding RNA predicted to be pseudogene by the Ensembl pipeline
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.
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.
non_stop_decay	Transcript that has 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.
retained_intron	Alternatively spliced transcript believed to contain intronic sequence relative to other, coding, variants.
protein_coding	Contains an open reading frame (ORF).
protein_coding_LoF	Not translated in the reference genome owing to a SNP/DIP but in other individuals/haplotypes/strains the transcript is translated. Replaces the polymorphic_pseudogene transcript biotype.
protein_coding_CDS_not_defined	Transcript that belongs to a protein_coding gene and doesn't contain an ORF. Replaces the processed_transcript transcript biotype in protein_coding genes.
processed_transcript	Doesn't contain an ORF.
non_coding	Transcript which is known from the literature to not be protein coding.
ambiguous_orf	Transcript believed to be protein coding, but with more than one possible open reading frame.
sense_intronic	Long non-coding transcript in introns of a coding gene that does not overlap any exons.
sense_overlapping	Long non-coding transcript that contains a coding gene in its intron on the same strand.
antisense/antisense_RNA	Has transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand.
known_ncrna
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 one of 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.
polymorphic_pseudogene	Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
retrotransposed	Pseudogene owing to a reverse transcribed and re-inserted sequence.
transcribed_processed_pseudogene transcribed_unprocessed_pseudogene transcribed_unitary_pseudogene	Pseudogene where protein homology or genomic structure indicates a pseudogene, but the presence of locus-specific transcripts indicates expression.
translated_processed_pseudogene translated_unprocessed_pseudogene	Pseudogene that has mass spec data suggesting that it is also translated.
unitary_pseudogene	A species-specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.
unprocessed_pseudogene	Pseudogene that can contain introns since produced by gene duplication.
artifact	Annotated on an artifactual region of the genome assembly.
lincRNA	Long, intervening noncoding (linc) RNA that can be found in evolutionarily conserved, intergenic regions.
macro_lncRNA	Unspliced lncRNA that is several kb in size.
3prime_overlapping_ncRNA	Transcript where ditag and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.
disrupted_domain	Otherwise viable coding region omitted from this alternatively spliced transcript because the splice variation affects a region coding for a protein domain.
vaultRNA/vault_RNA	Short non coding RNA gene that forms part of the vault ribonucleoprotein complex.
bidirectional_promoter_lncRNA	A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.